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00017 #include <qvbox.h>
00018 #include <qaccel.h>
00019 #include <qinputdialog.h>
00020 #include <qstring.h>
00021 #include <qtextview.h>
00022 #include <qdir.h>
00023 #include <qlayout.h>
00024 #include <qtooltip.h>
00025
00026
00027 #include <iostream>
00028 #include <set>
00029 #include <fstream>
00030
00031
00032 #include "trapperview.h"
00033 #include "trapperdoc.h"
00034 #include "trapper.h"
00035 #include "showmodesdlg.h"
00036 #include "trapperconf.h"
00037 #include "trapperparser.h"
00038 #include "macsimparser.h"
00039 #include "ChunkedXMLInputSource.h"
00040
00041 #include "filenew.xpm"
00042 #include "fileopen.xpm"
00043 #include "filesave.xpm"
00044 #include "editselectall.xpm"
00045
00046
00047 #include "zoom_in.xpm"
00048 #include "zoom_out.xpm"
00049 #include "zoom_in_x.xpm"
00050 #include "zoom_out_x.xpm"
00051 #include "zoom_in_y.xpm"
00052 #include "zoom_out_y.xpm"
00053 #include "dbflush.xpm"
00054 #include "dragbutton.xpm"
00055 #include "pointerbutton.xpm"
00056 #include "tcview.xpm"
00057 #include "tcnorm.xpm"
00058 #include "left_arrow.xpm"
00059 #include "right_arrow.xpm"
00060
00061
00062
00063 TrapperApp::TrapperApp()
00064 {
00065
00066 setCaption(tr("NGSView " "0.90" ) );
00067 dbenv = new DbEnv( DB_CXX_NO_EXCEPTIONS );
00068
00069
00070
00071 dbenv->set_cachesize(0, 8388608, 8);
00072 dbenv->set_lg_regionmax(524288);
00073 dbenv->set_lg_bsize(2097152);
00074
00075
00076 untitledCount=0;
00077 pDocList = new QList<TrapperDoc>();
00078 pDocList->setAutoDelete(true);
00079
00080
00081
00082 initView();
00083 initActions();
00084 initMenuBar();
00085 initToolBar();
00086 initStatusBar();
00087
00088 showMaximized();
00089
00090 viewToolBar->setOn(true);
00091 viewStatusBar->setOn(true);
00092
00093 projectDir = QString::null;
00094
00095
00096 connect(pWorkspace, SIGNAL(windowActivated(QWidget*)), this, SLOT(slotActivatedWindow(QWidget*)));
00097
00098
00099 }
00100
00101 TrapperApp::~TrapperApp()
00102 {
00103
00104 dbenv->close(0);
00105 }
00106
00107 void TrapperApp::initActions()
00108 {
00109 QPixmap openIcon, saveIcon, newIcon, selectAllIcon, zoomPlusIcon, zoomMinusIcon,
00110 zoomPlusIconX, zoomPlusIconY, zoomMinusIconX, zoomMinusIconY, flushIcon, dragIcon, pointerIcon,
00111 tcViewIcon, tcNormIcon, leftArrowIcon, rightArrowIcon;
00112
00113 newIcon = QPixmap(filenew);
00114 openIcon = QPixmap(fileopen);
00115 saveIcon = QPixmap(filesave);
00116 selectAllIcon = QPixmap( editselectall );
00117 zoomPlusIcon = QPixmap( zoom_in );
00118 zoomPlusIconX = QPixmap( zoom_in_x );
00119 zoomPlusIconY = QPixmap( zoom_in_y );
00120 zoomMinusIcon = QPixmap( zoom_out );
00121 zoomMinusIconX = QPixmap( zoom_out_x);
00122 zoomMinusIconY = QPixmap( zoom_out_y);
00123 flushIcon = QPixmap( dbflush );
00124 pointerIcon = QPixmap(pointerbutton);
00125 dragIcon = QPixmap(dragbutton);
00126 tcViewIcon = QPixmap(tcview);
00127 tcNormIcon = QPixmap(tcnorm);
00128 leftArrowIcon = QPixmap(left_arrow);
00129 rightArrowIcon = QPixmap(right_arrow);
00130
00131
00132 fileNew = new QAction(tr("New Project"), newIcon, tr("&New"), QAccel::stringToKey(tr("Ctrl+N")), this);
00133 fileNew->setStatusTip(tr("Creates a new project"));
00134 fileNew->setWhatsThis(tr("New Project\n\nCreates a new project"));
00135 connect(fileNew, SIGNAL(activated()), this, SLOT(slotFileNew()));
00136
00137 fileOpen = new QAction(tr("Open Contig"), openIcon, tr("&Open..."), QAccel::stringToKey(tr("Ctrl+O")), this);
00138 fileOpen->setStatusTip(tr("Opens an existing contig or creates a new one"));
00139 fileOpen->setWhatsThis(tr("Open Contig\n\nOpens an existing contig or creates a new one. To create a new contig, simply create a new directory in the file dialog and choose it"));
00140 connect(fileOpen, SIGNAL(activated()), this, SLOT(slotFileOpen()));
00141
00142 fileSave = new QAction(tr("Save File"), saveIcon, tr("&Save"), QAccel::stringToKey(tr("Ctrl+S")), this);
00143 fileSave->setStatusTip(tr("Saves the actual document"));
00144 fileSave->setWhatsThis(tr("Save File.\n\nSaves the actual document"));
00145 connect(fileSave, SIGNAL(activated()), this, SLOT(slotFileSave()));
00146
00147 fileSaveAs = new QAction(tr("Save File As"), tr("Save &as..."), 0, this);
00148 fileSaveAs->setStatusTip(tr("Saves the actual document under a new filename"));
00149 fileSaveAs->setWhatsThis(tr("Save As\n\nSaves the actual document under a new filename"));
00150 connect(fileSaveAs, SIGNAL(activated()), this, SLOT(slotFileSave()));
00151
00152 fileClose = new QAction(tr("Close Project"), tr("&Close"), QAccel::stringToKey(tr("Ctrl+W")), this);
00153 fileClose->setStatusTip(tr("Closes the actual project"));
00154 fileClose->setWhatsThis(tr("Close Project\n\nCloses the actual project"));
00155 connect(fileClose, SIGNAL(activated()), this, SLOT(slotFileClose()));
00156
00157 filePrint = new QAction(tr("Print File"), tr("&Print"), QAccel::stringToKey(tr("Ctrl+P")), this);
00158 filePrint->setStatusTip(tr("Prints out the actual document"));
00159 filePrint->setWhatsThis(tr("Print File\n\nPrints out the actual document"));
00160 connect(filePrint, SIGNAL(activated()), this, SLOT(slotFilePrint()));
00161
00162 fileQuit = new QAction(tr("Exit"), tr("E&xit"), QAccel::stringToKey(tr("Ctrl+Q")), this);
00163 fileQuit->setStatusTip(tr("Quits the application"));
00164 fileQuit->setWhatsThis(tr("Exit\n\nQuits the application"));
00165 connect(fileQuit, SIGNAL(activated()), this, SLOT(slotFileQuit()));
00166
00167 fileFlush = new QAction(tr("Flush"), flushIcon, tr("&Flush"), QAccel::stringToKey(tr("Ctrl+F")), this);
00168 fileFlush->setStatusTip(tr("Flushes cached data"));
00169 fileFlush->setWhatsThis(tr("Flush\n\nFlushes cached data to database"));
00170
00171
00172 editCut = new QAction(tr("Cut"), tr("Cu&t"), QAccel::stringToKey(tr("Ctrl+X")), this);
00173 editCut->setStatusTip(tr("Cuts the selected section and puts it to the clipboard"));
00174 editCut->setWhatsThis(tr("Cut\n\nCuts the selected section and puts it to the clipboard"));
00175 connect(editCut, SIGNAL(activated()), this, SLOT(slotEditCut()));
00176
00177 editCopy = new QAction(tr("Copy"), tr("&Copy"), QAccel::stringToKey(tr("Ctrl+C")), this);
00178 editCopy->setStatusTip(tr("Copies the selected section to the clipboard"));
00179 editCopy->setWhatsThis(tr("Copy\n\nCopies the selected section to the clipboard"));
00180 connect(editCopy, SIGNAL(activated()), this, SLOT(slotEditCopy()));
00181
00182 editUndo = new QAction(tr("Undo last move"), tr("&Undo last move"), QAccel::stringToKey(tr("Ctrl+Z")), this);
00183 editUndo->setStatusTip(tr("Reverts the last move"));
00184 editUndo->setWhatsThis(tr("Undo\n\nReverts the last read moving action"));
00185 connect(editUndo, SIGNAL(activated()), this, SLOT(slotEditUndo()));
00186
00187 editPaste = new QAction(tr("Paste"), tr("&Paste"), QAccel::stringToKey(tr("Ctrl+V")), this);
00188 editPaste->setStatusTip(tr("Pastes the clipboard contents to actual position"));
00189 editPaste->setWhatsThis(tr("Paste\n\nPastes the clipboard contents to actual position"));
00190 connect(editPaste, SIGNAL(activated()), this, SLOT(slotEditPaste()));
00191
00192 editSelectAll = new QAction(tr("Select All"), selectAllIcon, tr("Select &All"), QAccel::stringToKey(tr("Ctrl+A")), this);
00193 editSelectAll->setStatusTip(tr("Selects all reads"));
00194 editSelectAll->setWhatsThis(tr("Select All\n\nSelects all reads"));
00195 connect(editSelectAll, SIGNAL(activated()), this, SLOT(slotEditSelectAll()));
00196
00197 editSelectBetween = new QAction(tr("Select Between rows"), tr("Select &Between rows"), 0, this);
00198 editSelectBetween->setStatusTip(tr("Selects all reads between two rows"));
00199 editSelectBetween->setWhatsThis(tr("Select Between rows\n\nSelects all reads between two rows"));
00200 connect(editSelectBetween, SIGNAL(activated()), this, SLOT(slotEditSelectBetween()));
00201
00202 editSelectBetweenCols = new QAction(tr("Select Between cols"), tr("Select Between cols"), 0, this);
00203 editSelectBetweenCols->setStatusTip(tr("Selects all reads between two cols"));
00204 editSelectBetweenCols->setWhatsThis(tr("Select Between rows\n\nSelects all reads between two cols"));
00205 connect(editSelectBetweenCols, SIGNAL(activated()), this, SLOT(slotEditSelectBetweenCols()));
00206
00207 editFindRead = new QAction(tr("Find Read"), tr("Find Read"), 0, this);
00208 editFindRead->setStatusTip(tr("Selects a specific read"));
00209 editFindRead->setWhatsThis(tr("Find Read\n\nSelects a specific read"));
00210 connect(editFindRead, SIGNAL(activated()), this, SLOT(slotEditFindRead()));
00211
00212 editFindTag = new QAction(tr("Find Tag"), tr("Find Tag"), 0, this);
00213 editFindTag->setStatusTip(tr("Selects a specific tag"));
00214 editFindTag->setWhatsThis(tr("Find Tag\n\nSelects a specific tag"));
00215 connect(editFindTag, SIGNAL(activated()), this, SLOT(slotEditFindTag()));
00216
00217 viewToolBar = new QAction(tr("Toolbar"), tr("Tool&bar"), 0, this, 0, true);
00218 viewToolBar->setStatusTip(tr("Enables/disables the toolbar"));
00219 viewToolBar->setWhatsThis(tr("Toolbar\n\nEnables/disables the toolbar"));
00220 connect(viewToolBar, SIGNAL(toggled(bool)), this, SLOT(slotViewToolBar(bool)));
00221
00222 viewStatusBar = new QAction(tr("Statusbar"), tr("&Statusbar"), 0, this, 0, true);
00223 viewStatusBar->setStatusTip(tr("Enables/disables the statusbar"));
00224 viewStatusBar->setWhatsThis(tr("Statusbar\n\nEnables/disables the statusbar"));
00225 connect(viewStatusBar, SIGNAL(toggled(bool)), this, SLOT(slotViewStatusBar(bool)));
00226
00227 windowNewWindow = new QAction(tr("New Wiew"), tr("&New Wiew"), 0, this);
00228 windowNewWindow->setStatusTip(tr("Opens a new view for the current document"));
00229 windowNewWindow->setWhatsThis(tr("New Wiew\n\nOpens a new view for the current document"));
00230 connect(windowNewWindow, SIGNAL(activated()), this, SLOT(slotWindowNewWindow()));
00231
00232 windowCascade = new QAction(tr("Cascade"), tr("&Cascade"), 0, this);
00233 windowCascade->setStatusTip(tr("Cascades all windows"));
00234 windowCascade->setWhatsThis(tr("Cascade\n\nCascades all windows"));
00235 connect(windowCascade, SIGNAL(activated()), pWorkspace, SLOT(cascade()));
00236
00237 windowTile = new QAction(tr("Tile"), tr("&Tile"), 0, this);
00238 windowTile->setStatusTip(tr("Tiles all windows"));
00239 windowTile->setWhatsThis(tr("Tile\n\nTiles all windows"));
00240 connect(windowTile, SIGNAL(activated()), pWorkspace, SLOT(tile()));
00241
00242 windowAction = new QActionGroup(this, 0, false);
00243 windowAction->add(windowNewWindow);
00244 windowAction->add(windowCascade);
00245 windowAction->add(windowTile);
00246
00247 normalModeAction = new QAction(tr("Normal mode"), pointerIcon, tr("Normal mode"), 0, this);
00248 normalModeAction->setStatusTip(tr("Sets mode to normal"));
00249 normalModeAction->setWhatsThis(tr("Normal mode\n\nFor selection of reads, normal moving etc"));
00250 normalModeAction->setToggleAction(true);
00251 normalModeAction->setOn(true);
00252 connect(normalModeAction, SIGNAL(activated()), this, SLOT(slotNormalMode()));
00253
00254 dragModeAction = new QAction(tr("Drag mode"), dragIcon, tr("Drag mode"), 0, this);
00255 dragModeAction->setStatusTip(tr("Sets mode to drag mode"));
00256 dragModeAction->setWhatsThis(tr("Drag mode\n\nFor moving reads between contigs, and sideways moving"));
00257 dragModeAction->setToggleAction(true);
00258 connect(dragModeAction, SIGNAL(activated()), this, SLOT(slotDragMode()));
00259
00260 modeActionGroup = new QActionGroup(this, 0, true);
00261 modeActionGroup->add(normalModeAction);
00262 modeActionGroup->add(dragModeAction);
00263
00264 timecourseAction = new QAction(tr("View Time Course data"), tcViewIcon, tr("Time Course"), 0, this);
00265 timecourseAction->setStatusTip(tr("Enables Time Course viewing"));
00266 timecourseAction->setWhatsThis(tr("Time Course\n\nFor viewing of time course data"));
00267 timecourseAction->setToggleAction(true);
00268 timecourseAction->setOn(false);
00269 connect(timecourseAction, SIGNAL(toggled(bool)), this, SLOT(slotViewTimeCourse(bool)));
00270
00271 normalizeAction = new QAction(tr("View Time Course data normalized"), tcNormIcon, tr("Normalized Time Course"), 0, this);
00272 normalizeAction->setStatusTip(tr("Normalize Time Course viewing"));
00273 normalizeAction->setWhatsThis(tr("Normalize Time Course\n\nFor viewing of time course data normalized for each individual read"));
00274 normalizeAction->setToggleAction(true);
00275 normalizeAction->setOn(false);
00276 normalizeAction->setEnabled(false);
00277 connect(normalizeAction, SIGNAL(toggled(bool)), this, SLOT(slotNormalizeTimeCourse(bool)));
00278 connect(timecourseAction, SIGNAL(toggled(bool)), normalizeAction, SLOT(setEnabled(bool)));
00279
00280 timecourseActionGroup = new QActionGroup(this, 0, false);
00281 timecourseActionGroup->add(timecourseAction);
00282 timecourseActionGroup->add(normalizeAction);
00283
00284 clusterScrollForwardAction = new QAction(tr("Scroll Right"), rightArrowIcon, tr("Scroll Right"), ALT + Key_Right, this);
00285 clusterScrollForwardAction->setStatusTip(tr("Scrolls right to next cluster"));
00286 clusterScrollForwardAction->setWhatsThis(tr("Scrolls right to next cluster"));
00287 connect(clusterScrollForwardAction, SIGNAL(activated()), this, SLOT(slotScrollForward()));
00288
00289 clusterScrollBackwardsAction = new QAction(tr("Scroll Left"), leftArrowIcon, tr("Scroll Left"), ALT + Key_Left, this);
00290 clusterScrollBackwardsAction->setStatusTip(tr("Scrolls left to previous cluster"));
00291 clusterScrollBackwardsAction->setWhatsThis(tr("Scrolls left to previous cluster"));
00292 connect(clusterScrollBackwardsAction, SIGNAL(activated()), this, SLOT(slotScrollBackwards()));
00293
00294
00295
00296
00297
00298
00299
00300
00301
00302 helpAboutApp = new QAction(tr("About"), tr("&About..."), 0, this);
00303 helpAboutApp->setStatusTip(tr("About the application"));
00304 helpAboutApp->setWhatsThis(tr("About\n\nAbout the application"));
00305 connect(helpAboutApp, SIGNAL(activated()), this, SLOT(slotHelpAbout()));
00306
00307
00308
00309
00310
00311
00312
00313
00314
00315
00316
00317 importNewAction = new QAction(tr("Import project"), tr("&Import project"), 0, this);
00318 importNewAction->setStatusTip(tr("Imports project data"));
00319 importNewAction->setWhatsThis(tr("Imports project data"));
00320 connect(importNewAction, SIGNAL(activated()), this, SLOT(slotNewImport()));
00321
00322 importChromatAction = new QAction(tr("Import Chromatograms"), tr("Import Chromatograms"), 0, this);
00323 importChromatAction->setStatusTip(tr("Imports chromatogram data"));
00324 importChromatAction->setWhatsThis(tr("Imports chromatogram data"));
00325 connect(importChromatAction, SIGNAL(activated()), this, SLOT(slotChromatImport()));
00326
00327 importMateAction = new QAction(tr("Import Mate pairs"), tr("Import Mate Pairs"), 0, this);
00328 importMateAction->setStatusTip(tr("Imports mate pair data"));
00329 importMateAction->setWhatsThis(tr("Imports mate pair data"));
00330 connect(importMateAction, SIGNAL(activated()), this, SLOT(slotMateImport()));
00331
00332 importTcAction = new QAction(tr("Import Time Course Data"), tr("Import Time Course"), 0, this);
00333 importTcAction->setStatusTip(tr("Imports Time Course Data"));
00334 importTcAction->setWhatsThis(tr("Imports Time Course Data"));
00335 connect(importTcAction, SIGNAL(activated()), this, SLOT(slotTcImport()));
00336
00337 importPhdAction = new QAction(tr("Import phd data"), tr("Import phd data"), 0, this);
00338 importPhdAction->setStatusTip(tr("Imports phd data"));
00339 importPhdAction->setWhatsThis(tr("Imports phd data"));
00340 connect(importPhdAction, SIGNAL(activated()), this, SLOT(slotPhdImport()));
00341
00342 exportAction = new QAction(tr("Export"), tr("&Export"), 0, this);
00343 exportAction->setStatusTip(tr("Exports data"));
00344 exportAction->setWhatsThis(tr("Exports data"));
00345 connect(exportAction, SIGNAL(activated()), this, SLOT(slotExport()));
00346
00347 zoomInAction = new QAction(tr("Zoom in"), zoomPlusIcon, tr("Zoom in"), Key_Plus, this);
00348 zoomInAction->setStatusTip(tr("Zooms in"));
00349 zoomInAction->setWhatsThis(tr("Zooms in"));
00350 connect(zoomInAction, SIGNAL(activated()), this, SLOT(slotZoomIn()));
00351
00352 zoomInXAction = new QAction(tr("Zoom in X"), zoomPlusIconX, tr("Zoom in X"),CTRL + Key_Plus, this);
00353 zoomInXAction->setStatusTip(tr("Zooms in X"));
00354 zoomInXAction->setWhatsThis(tr("Zooms in X direction"));
00355 connect(zoomInXAction, SIGNAL(activated()), this, SLOT(slotZoomInX()));
00356
00357 zoomInYAction = new QAction(tr("Zoom in Y"), zoomPlusIconY, tr("Zoom in Y"), CTRL + ALT + Key_Plus, this);
00358 zoomInYAction->setStatusTip(tr("Zooms in Y"));
00359 zoomInYAction->setWhatsThis(tr("Zooms in Y direction"));
00360 connect(zoomInYAction, SIGNAL(activated()), this, SLOT(slotZoomInY()));
00361
00362 zoomOutAction = new QAction(tr("Zoom out"), zoomMinusIcon, tr("&Zoom out"), Key_Minus, this);
00363 zoomOutAction->setStatusTip(tr("Zooms out"));
00364 zoomOutAction->setWhatsThis(tr("Zooms out"));
00365 connect(zoomOutAction, SIGNAL(activated()), this, SLOT(slotZoomOut()));
00366
00367 zoomOutXAction = new QAction(tr("Zoom out X"), zoomMinusIconX, tr("Zoom out X"), CTRL + Key_Minus, this);
00368 zoomOutXAction->setStatusTip(tr("Zooms out X"));
00369 zoomOutXAction->setWhatsThis(tr("Zooms out in X direction"));
00370 connect(zoomOutXAction, SIGNAL(activated()), this, SLOT(slotZoomOutX()));
00371
00372 zoomOutYAction = new QAction(tr("Zoom out Y"), zoomMinusIconY, tr("Zoom out Y"), CTRL + ALT + Key_Minus, this);
00373 zoomOutYAction->setStatusTip(tr("Zooms out Y"));
00374 zoomOutYAction->setWhatsThis(tr("Zooms out in Y direction"));
00375 connect(zoomOutYAction, SIGNAL(activated()), this, SLOT(slotZoomOutY()));
00376
00377 enlargeAction = new QAction(tr("Enlarge"), tr("&Enlarge"), 0, this);
00378 enlargeAction->setStatusTip(tr("Adds more viewable rows"));
00379 enlargeAction->setWhatsThis(tr("Enlarges view, so that more rows and columns can be displayed"));
00380 connect(enlargeAction, SIGNAL(activated()), this, SLOT(slotEnlarge()));
00381
00382 shrinkAction = new QAction(tr("Shrink"), tr("&Shrink"), 0, this);
00383 shrinkAction->setStatusTip(tr("Removes viewable rows. Does not affect data."));
00384 shrinkAction->setWhatsThis(tr("Shrinks view, displaying fewer rows and columns. Does not affect data."));
00385 connect(shrinkAction, SIGNAL(activated()), this, SLOT(slotShrink()));
00386
00387 showStatisticsAction = new QAction(tr("Show statistics"), tr("Show statistics"), 0, this);
00388 showStatisticsAction->setStatusTip(tr("Show statistics about contig"));
00389 showStatisticsAction->setWhatsThis(tr("Show underlying berkeley db statistics for this contig"));
00390 connect(showStatisticsAction, SIGNAL(activated()), this, SLOT(slotShowStatistics()));
00391
00392 configureViewModesAction = new QAction(tr("Configure view modes"), tr("&Configure modes"), 0, this);
00393 configureViewModesAction->setStatusTip(tr("Configure view modes"));
00394 configureViewModesAction->setWhatsThis(tr("Configure view modes"));
00395 connect(configureViewModesAction, SIGNAL(activated()), this, SLOT(slotConfigureViewModes()));
00396
00397
00398 }
00399
00400 void TrapperApp::initMenuBar()
00401 {
00402
00403
00404
00405
00406
00407 pFileMenu=new QPopupMenu();
00408
00409 fileOpen->addTo(pFileMenu);
00410 fileClose->addTo(pFileMenu);
00411
00412
00413
00414
00415
00416
00417 pFileMenu->insertSeparator();
00418 fileQuit->addTo(pFileMenu);
00419
00420
00421
00422
00423
00424
00425 pEditMenu=new QPopupMenu();
00426 editUndo->addTo(pEditMenu);
00427
00428 editCut->addTo(pEditMenu);
00429 editCopy->addTo(pEditMenu);
00430 editPaste->addTo(pEditMenu);
00431 editSelectAll->addTo(pEditMenu);
00432 editSelectBetween->addTo(pEditMenu);
00433 editSelectBetweenCols->addTo(pEditMenu);
00434 editFindRead->addTo(pEditMenu);
00435 editFindTag->addTo(pEditMenu);
00436
00437
00438
00439 pViewMenu=new QPopupMenu();
00440 pViewMenu->setCheckable(true);
00441 viewToolBar->addTo(pViewMenu);
00442 viewStatusBar->addTo(pViewMenu);
00443
00444 zoomInAction->addTo(pViewMenu);
00445 zoomOutAction->addTo(pViewMenu);
00446 zoomInXAction->addTo(pViewMenu);
00447 zoomOutXAction->addTo(pViewMenu);
00448 zoomInYAction->addTo(pViewMenu);
00449 zoomOutYAction->addTo(pViewMenu);
00450
00451
00452 showStatisticsAction->addTo(pViewMenu);
00453 timecourseActionGroup->addTo(pViewMenu);
00454
00455
00456
00457
00458
00459 pToolsMenu=new QPopupMenu();
00460
00461 importNewAction->addTo(pToolsMenu);
00462
00463 importMateAction->addTo(pToolsMenu);
00464 importTcAction->addTo(pToolsMenu);
00465
00466 modeActionGroup->addTo(pToolsMenu);
00467 exportAction->addTo(pToolsMenu);
00468
00469
00470
00471 pWindowMenu = new QPopupMenu(this);
00472 pWindowMenu->setCheckable(true);
00473 connect(pWindowMenu, SIGNAL(aboutToShow()), this, SLOT(windowMenuAboutToShow()));
00474
00475
00476
00477 pHelpMenu=new QPopupMenu();
00478
00479 helpAboutApp->addTo(pHelpMenu);
00480 pHelpMenu->insertSeparator();
00481 pHelpMenu->insertItem(tr("What's &This"), this, SLOT(whatsThis()), SHIFT+Key_F1);
00482
00483 menuBar()->insertItem(tr("&Contig"), pFileMenu);
00484 menuBar()->insertItem(tr("&Edit"), pEditMenu);
00485 menuBar()->insertItem(tr("&View"), pViewMenu);
00486 menuBar()->insertItem(tr("&Window"), pWindowMenu);
00487 menuBar()->insertItem(tr("&Tools"), pToolsMenu);
00488 menuBar()->insertItem(tr("&Help"), pHelpMenu);
00489
00490 }
00491
00492 void TrapperApp::initToolBar()
00493 {
00494
00495
00496 fileToolbar = new QToolBar(this, "file operations");
00497
00498 fileOpen->addTo(fileToolbar);
00499
00500
00501 editSelectAll->addTo(fileToolbar);
00502 zoomInAction->addTo(fileToolbar);
00503 zoomOutAction->addTo(fileToolbar);
00504 zoomInXAction->addTo(fileToolbar);
00505 zoomOutXAction->addTo(fileToolbar);
00506 zoomInYAction->addTo(fileToolbar);
00507 zoomOutYAction->addTo(fileToolbar);
00508
00509 fileToolbar->addSeparator();
00510 modeActionGroup->addTo(fileToolbar);
00511 fileToolbar->addSeparator();
00512 timecourseActionGroup->addTo(fileToolbar);
00513 fileToolbar->addSeparator();
00514
00515
00516 clusterWindowBox = new QSpinBox(1, numeric_limits<int>::max(), 1, fileToolbar);
00517 clusterWindowBox->setValue(100);
00518 connect(clusterWindowBox, SIGNAL(valueChanged(int)), this, SLOT(slotClusterWindowChanged(int)));
00519 QToolTip::add(clusterWindowBox, "Window size for cluster scrolling");
00520
00521 clusterMinNumBox = new QSpinBox(1, numeric_limits<int>::max(), 1, fileToolbar);
00522 clusterMinNumBox->setValue(10);
00523 connect(clusterMinNumBox, SIGNAL(valueChanged(int)), this, SLOT(slotClusterNumChanged(int)));
00524 QToolTip::add(clusterMinNumBox, "Min number of tags in window for cluster scrolling");
00525
00526 clusterScrollBackwardsAction->addTo(fileToolbar);
00527 clusterScrollForwardAction->addTo(fileToolbar);
00528 fileToolbar->addSeparator();
00529
00530 QWhatsThis::whatsThisButton(fileToolbar);
00531 }
00532
00533 void TrapperApp::initStatusBar()
00534 {
00535
00536
00537 statusBar()->message(tr("Ready."));
00538 }
00539
00540 void TrapperApp::initView()
00541 {
00542
00543
00544 QVBox* view_back = new QVBox( this );
00545 view_back->setFrameStyle( QFrame::StyledPanel | QFrame::Sunken );
00546 pWorkspace = new QWorkspace( view_back );
00547 setCentralWidget(view_back);
00548 }
00549
00550 void TrapperApp::createClient(TrapperDoc* doc, QString modeView )
00551 {
00552
00553 TrapperView* w = new TrapperView(doc, pWorkspace, modeView, modeView);
00554 w->installEventFilter(this);
00555 doc->addView(w);
00556 connect( w, SIGNAL( message( const QString& ) ), statusBar(), SLOT( message( const QString& ) ) );
00557
00558
00559 connect( w, SIGNAL( createView( QString ) ), this, SLOT( slotCreateClient( QString ) ) );
00560 if ( pWorkspace->windowList().isEmpty() )
00561 w->showMaximized();
00562 else
00563 w->show();
00564 }
00565
00566 void TrapperApp::slotCreateClient( QString modeView )
00567 {
00568 cerr<<"I suspect I never get called...???"<<endl;
00569 statusBar()->message(tr("Opening new view ..."));
00570
00571 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
00572 if( m )
00573 {
00574 TrapperDoc* doc = m->getDocument();
00575 createClient( doc, modeView );
00576 }
00577 statusBar()->message(tr("Ready."));
00578 }
00579
00580 void TrapperApp::openDocumentFile(const char* file)
00581 {
00582 statusBar()->message(tr("Opening file..."));
00583
00584 TrapperDoc* doc;
00585
00586 for(doc=pDocList->first(); doc > 0; doc=pDocList->next()) {
00587
00588
00589 if(doc->pathName() == file) {
00590 TrapperView* view=doc->firstView();
00591 view->setFocus();
00592 return;
00593 }
00594 }
00595 doc = new TrapperDoc(dbenv);
00596 pDocList->append(doc);
00597 doc->newDocument();
00598
00599
00600
00601 QString fileName;
00602 if(!file)
00603 {
00604 untitledCount+=1;
00605 fileName=QString(tr("%1/Untitled%2")).arg(projectDir).arg(untitledCount);
00606
00607
00608
00609 }
00610 else
00611 {
00612 fileName = file;
00613 }
00614
00615 if(!doc->openDocument(fileName))
00616 {
00617 QMessageBox::critical(this, tr("Error !"),tr("Could not open document !"));
00618 delete doc;
00619 return;
00620 }
00621
00622
00623
00624
00625
00626
00627 createClient(doc, QString("closeup"));
00628
00629
00630 statusBar()->message(tr("Ready."));
00631 }
00632
00633 bool TrapperApp::queryExit()
00634 {
00635 int exit=QMessageBox::information(this, tr("Quit..."),
00636 tr("Do your really want to quit?"),
00637 QMessageBox::Ok, QMessageBox::Cancel);
00638
00639 if (exit==1)
00640 {}
00641 else
00642 {}
00643 ;
00644
00645 return (exit==1);
00646 }
00647
00648 bool TrapperApp::eventFilter(QObject* object, QEvent* event)
00649 {
00650 if((event->type() == QEvent::Close) && ((TrapperApp*)object!=this) ) {
00651
00652 QCloseEvent* e = (QCloseEvent*)event;
00653 TrapperView* pView = (TrapperView*)object;
00654 TrapperDoc* pDoc = pView->getDocument();
00655 if(pDoc->canCloseFrame(pView)) {
00656 pDoc->removeView(pView);
00657 if( !pDoc->firstView() ) {
00658 pDocList->remove(pDoc);
00659 }
00660
00661 e->accept();
00662
00663 }
00664 else {
00665 e->ignore();
00666 }
00667 return true;
00668 }
00669 else if ( (event->type() == QEvent::KeyPress) ) {
00670 QKeyEvent* e = (QKeyEvent*)event;
00671 int scrollfactor(10);
00672 if ( e->state() == Qt::ControlButton )
00673 scrollfactor *= 10;
00674
00675 if ( e->key() == Qt::Key_Up ) {
00676 scroll(0, -1*scrollfactor);
00677 e->accept();
00678 return true;
00679 }
00680 else if ( e->key() == Qt::Key_Down ) {
00681 scroll(0, 1*scrollfactor);
00682 e->accept();
00683 return true;
00684 }
00685 else if ( e->key() == Qt::Key_Left ) {
00686 scroll(-1*scrollfactor, 0);
00687 e->accept();
00688 return true;
00689 }
00690 else if ( e->key() == Qt::Key_Right ) {
00691 scroll(1*scrollfactor, 0);
00692 e->accept();
00693 return true;
00694 }
00695 else if ( e->key() == Qt::Key_Tab ) {
00696 pWorkspace->activateNextWindow();
00697 e->accept();
00698 return true;
00699 }
00700 else if ( e->key() == Qt::Key_Backtab ) {
00701 pWorkspace->activatePrevWindow();
00702 e->accept();
00703 return true;
00704 }
00705
00706 e->ignore();
00707 }
00708
00709
00710 return QWidget::eventFilter( object, event );
00711 }
00712
00713
00714
00715
00716
00717 void TrapperApp::slotFileNew()
00718 {
00719 statusBar()->message(tr("Creating new file..."));
00720
00721 openDocumentFile();
00722
00723 statusBar()->message(tr("Ready."));
00724 }
00725
00726 void TrapperApp::slotFileOpen()
00727 {
00728 statusBar()->message(tr("Opening file..."));
00729
00730 QString dirName = QFileDialog::getExistingDirectory(projectDir,this,"contig dir selection","Choose contig dir");
00731 if (!dirName.isEmpty())
00732 {
00733 QDir d(dirName), projdir(projectDir);
00734
00735 if ( !d.cdUp() || d!= projdir ) {
00736 QMessageBox::critical(this, tr("Error !"),tr("Contig directory must be a subdirectory of project directory!"));
00737
00738 }
00739 else {
00740
00741 openDocumentFile(dirName);
00742 }
00743 }
00744 statusBar()->message(tr("Ready."));
00745 }
00746
00747
00748 void TrapperApp::slotFileSave()
00749 {
00750 statusBar()->message(tr("Saving file..."));
00751
00752 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
00753 if( m )
00754 {
00755 TrapperDoc* doc = m->getDocument();
00756 if(doc->title().contains(tr("Untitled")))
00757 slotFileSaveAs();
00758 else
00759 if(!doc->saveDocument(doc->pathName()))
00760 QMessageBox::critical (this, tr("I/O Error !"), tr("Could not save the current document !"));
00761 }
00762
00763 statusBar()->message(tr("Ready."));
00764 }
00765
00766 void TrapperApp::slotFileSaveAs()
00767 {
00768 statusBar()->message(tr("Saving file under new filename..."));
00769 QString fn = QFileDialog::getSaveFileName(0, 0, this);
00770 if (!fn.isEmpty())
00771 {
00772 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
00773 if( m )
00774 {
00775 TrapperDoc* doc = m->getDocument();
00776 if(!doc->saveDocument(fn))
00777 {
00778 QMessageBox::critical (this, tr("I/O Error !"), tr("Could not save the current document !"));
00779 return;
00780 }
00781 doc->changedViewList();
00782 }
00783 }
00784 statusBar()->message(tr("Ready."));
00785 }
00786 void TrapperApp::slotFileFlush()
00787 {
00788 statusBar()->message(tr("Flushing database caches..."));
00789
00790 for(TrapperDoc * doc=pDocList->first(); doc!= 0; doc=pDocList->next())
00791 {
00792 cerr<<"doc->pathName(): "<<doc->pathName()<<endl;
00793 list<string> type_list = GeneralMaker::listRegistered();
00794 for( list<string>::iterator it = type_list.begin(); it != type_list.end(); ++it ) {
00795 TrDb* db = doc->findTrDb( *it );
00796 if ( db ) {
00797 cerr<<"Syncing "<<*it<<endl;
00798 db->sync();
00799
00800 }
00801 }
00802 }
00803 statusBar()->message(tr("Ready."));
00804 }
00805
00806 void TrapperApp::slotFileClose()
00807 {
00808 cerr<<"Hello slotFileClose() "<<endl;
00809
00810 statusBar()->message(tr("Closing file..."));
00811
00812 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
00813 if( m )
00814 {
00815 TrapperDoc* doc=m->getDocument();
00816 doc->closeDocument();
00817 }
00818
00819 statusBar()->message(tr("Ready."));
00820 cerr<<"Bye slotFileClose() "<<endl;
00821 }
00822
00823 void TrapperApp::slotFilePrint()
00824 {
00825 statusBar()->message(tr("Printing..."));
00826
00827 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00828 if ( m )
00829 m->print( printer );
00830
00831 statusBar()->message(tr("Ready."));
00832 }
00833
00834 void TrapperApp::slotFileQuit()
00835 {
00836 statusBar()->message(tr("Exiting application..."));
00837
00838 for(TrapperDoc * doc=pDocList->first(); doc > 0; doc=pDocList->next())
00839 {
00840 delete doc;
00841 }
00842
00843
00844
00845
00846
00847
00848
00849
00850
00851
00852
00853
00854
00855
00856
00857
00858
00859 qApp->quit();
00860
00861
00862
00863
00864
00865
00866
00867
00868 statusBar()->message(tr("Ready."));
00869 }
00870
00871 void TrapperApp::slotEditUndo()
00872 {
00873 statusBar()->message(tr("Reverting last move..."));
00874
00875 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00876 if ( m ) m->undo();
00877
00878 statusBar()->message(tr("Ready."));
00879 }
00880
00881 void TrapperApp::slotEditCut()
00882 {
00883 statusBar()->message(tr("Cutting selection..."));
00884
00885 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00886 if ( m ) m->cut();
00887
00888 statusBar()->message(tr("Ready."));
00889 }
00890
00891 void TrapperApp::slotEditCopy()
00892 {
00893 statusBar()->message(tr("Copying selection to clipboard..."));
00894
00895 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00896 if ( m ) m->copy();
00897
00898 statusBar()->message(tr("Ready."));
00899 }
00900
00901 void TrapperApp::slotEditPaste()
00902 {
00903 statusBar()->message(tr("Inserting clipboard contents..."));
00904
00905 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00906 if ( m ) m->paste();
00907 statusBar()->message(tr("Ready."));
00908 }
00909
00910 void TrapperApp::slotEditSelectAll()
00911 {
00912 statusBar()->message(tr("Selecting all reads..."));
00913
00914 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00915 if ( m ) m->selectAll();
00916 statusBar()->message(tr("Ready."));
00917 }
00918
00919 void TrapperApp::slotEditSelectBetween()
00920 {
00921 statusBar()->message(tr("Selecting all reads between rows..."));
00922
00923 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00924 if ( m ) m->selectBetween();
00925 statusBar()->message(tr("Ready."));
00926 }
00927
00928 void TrapperApp::slotEditSelectBetweenCols()
00929 {
00930 statusBar()->message(tr("Selecting all reads between cols..."));
00931
00932 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00933 if ( m ) m->selectBetweenCols();
00934 statusBar()->message(tr("Ready."));
00935 }
00936
00937 void TrapperApp::slotEditFindRead()
00938 {
00939 statusBar()->message(tr("Finding read..."));
00940
00941 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00942 if ( m ) m->findRead();
00943 statusBar()->message(tr("Ready."));
00944 }
00945
00946 void TrapperApp::slotEditFindTag()
00947 {
00948 statusBar()->message(tr("Finding tag..."));
00949
00950 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00951 if ( m ) m->findTag();
00952 statusBar()->message(tr("Ready."));
00953 }
00954
00955 void TrapperApp::slotViewToolBar(bool toggle)
00956 {
00957 statusBar()->message(tr("Toggle toolbar..."));
00958
00959
00960 if (toggle== false)
00961 {
00962 fileToolbar->hide();
00963 }
00964 else
00965 {
00966 fileToolbar->show();
00967 };
00968 statusBar()->message(tr("Ready."));
00969 }
00970
00971 void TrapperApp::slotViewStatusBar(bool toggle)
00972 {
00973 statusBar()->message(tr("Toggle statusbar..."));
00974
00975
00976
00977 if (toggle == false)
00978 {
00979 statusBar()->hide();
00980 }
00981 else
00982 {
00983 statusBar()->show();
00984 }
00985 statusBar()->message(tr("Ready."));
00986 }
00987
00988 void TrapperApp::slotWindowNewWindow()
00989 {
00990 statusBar()->message(tr("Opening new document view..."));
00991
00992 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
00993 if ( m )
00994 {
00995 TrapperDoc* doc = m->getDocument();
00996 createClient(doc);
00997 }
00998 statusBar()->message(tr("Ready."));
00999 }
01000
01001 void TrapperApp::slotHelpAbout()
01002 {
01003 QMessageBox::about(this,tr("About..."),
01004 tr("NGSView\nVersion 1.0"
01005 "\n(c) 2003 - 2009 by Erik Arner, Martti Tammi, and Erik Sjölund"));
01006 }
01007
01008 void TrapperApp::slotHelpManual()
01009 {
01010 QMessageBox::about(this,tr("Help"),
01011 tr("Please see documentation included with DNPTrapper release or at http://dnptrapper.sourceforge.net"));
01012
01013 }
01014
01015 void TrapperApp::slotStatusHelpMsg(const QString &text)
01016 {
01017
01018
01019 statusBar()->message(text, 2000);
01020 }
01021
01022 void TrapperApp::windowMenuAboutToShow()
01023 {
01024 pWindowMenu->clear();
01025 windowNewWindow->addTo(pWindowMenu);
01026 windowCascade->addTo(pWindowMenu);
01027 windowTile->addTo(pWindowMenu);
01028
01029 if ( pWorkspace->windowList().isEmpty() )
01030 {
01031 windowAction->setEnabled(false);
01032 }
01033 else
01034 {
01035 windowAction->setEnabled(true);
01036 }
01037
01038 pWindowMenu->insertSeparator();
01039
01040 QWidgetList windows = pWorkspace->windowList();
01041 for ( int i = 0; i < int(windows.count()); ++i )
01042 {
01043 int id = pWindowMenu->insertItem(QString("&%1 ").arg(i+1)+windows.at(i)->caption(), this, SLOT( windowMenuActivated( int ) ) );
01044 pWindowMenu->setItemParameter( id, i );
01045 pWindowMenu->setItemChecked( id, pWorkspace->activeWindow() == windows.at(i) );
01046 }
01047 }
01048
01049 void TrapperApp::windowMenuActivated( int id )
01050 {
01051 QWidget* w = pWorkspace->windowList().at( id );
01052 if ( w )
01053 w->setFocus();
01054 }
01055
01056 void TrapperApp::slotZoomIn()
01057 {
01058 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01059 if( m )
01060 {
01061 m->zoomIn();
01062
01063 }
01064 }
01065
01066 void TrapperApp::slotZoomInX()
01067 {
01068 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01069 if( m )
01070 {
01071 m->zoomInX();
01072
01073 }
01074 }
01075
01076 void TrapperApp::slotZoomInY()
01077 {
01078 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01079 if( m )
01080 {
01081 m->zoomInY();
01082
01083 }
01084 }
01085
01086 void TrapperApp::slotZoomOut()
01087 {
01088 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01089 if( m )
01090 {
01091 m->zoomOut();
01092
01093 }
01094 }
01095
01096 void TrapperApp::slotZoomOutX()
01097 {
01098 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01099 if( m )
01100 {
01101 m->zoomOutX();
01102
01103 }
01104 }
01105
01106 void TrapperApp::slotZoomOutY()
01107 {
01108 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01109 if( m )
01110 {
01111 m->zoomOutY();
01112
01113 }
01114 }
01115
01116 void TrapperApp::slotEnlarge()
01117 {
01118 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01119 if( m )
01120 {
01121 m->enlarge();
01122 }
01123 }
01124
01125 void TrapperApp::slotShrink()
01126 {
01127 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01128 if( m )
01129 {
01130 m->shrink();
01131 }
01132 }
01133
01134 void TrapperApp::slotImport()
01135 {
01136 statusBar()->message(tr("Importing data from an xml file..."));
01137 QString fn = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose your xml file to import from");
01138 if (!fn.isEmpty()) {
01139 QFile f( fn );
01140 if ( !f.open( IO_ReadOnly ) ) {
01141 QMessageBox::warning(this,"","couldn't read file");
01142 }
01143
01144 QDomDocument domDoc("Trapper");
01145 if ( !domDoc.setContent( &f ) ) {
01146 f.close();
01147 QMessageBox::warning(this,"","couldn't read xml");
01148 return;
01149 }
01150 f.close();
01151
01152 QDomElement docElem = domDoc.documentElement();
01153
01154 for( QDomNode node1 = docElem.firstChild(); !node1.isNull() ; node1 = node1.nextSibling()) {
01155 if ( node1.isElement() && node1.nodeName() == "contig" ) {
01156 QDomElement elem1 = node1.toElement();
01157
01158 Q_ASSERT((elem1.hasAttribute("name")));
01159 QString contigName = elem1.attribute( "name");
01160
01161
01162 bool found = false;
01163
01164
01165
01166
01167
01168
01169
01170
01171
01172
01173
01174 QStringList contigNamesAlreadyPresent = contigNamesInProjectDir();
01175 if ( contigNamesAlreadyPresent.contains( contigName ) ) {
01176 found = true;
01177 }
01178 if ( found ) {
01179 QString message;
01180 message = QString("The contig name \"%1\" was specified in the import file, but that contig is already present in the project dir. Skipping this one").arg(contigName);
01181 QMessageBox::warning(this,"",message);
01182 continue;
01183 }
01184 QString fName = projectDir + "/" + contigName;
01185 TrapperDoc * tdoc = new TrapperDoc(dbenv);
01186 tdoc->openDocument(fName);
01187 tdoc->import( elem1 );
01188 delete tdoc;
01189 tdoc = NULL;
01190 cerr << "reached after"<<endl;
01191
01192 }
01193
01194 }
01195
01196
01197
01198
01199
01200
01201
01202
01203
01204
01205
01206
01207
01208
01209 }
01210 statusBar()->message(tr("Ready."));
01211 }
01212
01213 void TrapperApp::slotNewImport()
01214 {
01215 statusBar()->message(tr("Importing data from an xml file..."));
01216 QString fn = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose trapper xml or macsim file to import from");
01217 if (!fn.isEmpty()) {
01218 QFile f( fn );
01219 if ( !f.open( IO_ReadOnly ) ) {
01220 QMessageBox::warning(this,"","couldn't open file");
01221 return;
01222 }
01223 QXmlDefaultHandler* handler;
01224
01225
01226
01227 if ( fn.endsWith("macsim")) {
01228 handler = new MacsimParser(dbenv, projectDir);
01229 }
01230 else {
01231 handler = new TrapperParser(dbenv, projectDir);
01232 }
01233
01234
01235
01236
01237 QXmlInputSource* source = new ChunkedXMLInputSource( &f );
01238 QXmlSimpleReader reader;
01239 reader.setContentHandler( handler );
01240
01241
01242
01243
01244
01245
01246 int num_chunks(0);
01247 reader.parse( source, true );
01248 while ( reader.parseContinue() ) {
01249 num_chunks++;
01250
01251 }
01252 delete source;
01253
01254 }
01255 statusBar()->message(tr("Ready."));
01256 }
01257
01258 void TrapperApp::slotChromatImport()
01259 {
01260 statusBar()->message(tr("Importing chromatogram data..."));
01261
01262 QString chromatDirName = QFileDialog::getExistingDirectory(projectDir,this,"chromat dir selection","Choose chromatogram directory");
01263
01264 if (chromatDirName.isEmpty()) {
01265 return;
01266 }
01267
01268
01269
01270 QPtrList<TrapperDoc> docListNotAlreadyOpen;
01271 docListNotAlreadyOpen.setAutoDelete(true);
01272
01273 open_docs_not_already_open( docListNotAlreadyOpen );
01274
01275 for (TrapperDoc* doc = pDocList->first(); doc != 0; doc = pDocList->next() ) {
01276 doc->importChromat(chromatDirName);
01277 }
01278 for (TrapperDoc* doc = docListNotAlreadyOpen.first(); doc != 0; doc = docListNotAlreadyOpen.next() ) {
01279 doc->importChromat(chromatDirName);
01280 }
01281
01282
01283
01284 statusBar()->message(tr("Ready."));
01285 }
01286
01287 void TrapperApp::slotMateImport()
01288 {
01289 statusBar()->message(tr("Importing mate data..."));
01290
01291 QString matefile = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose your mate pair file to import from");
01292
01293 if (matefile.isEmpty()) {
01294 return;
01295 }
01296
01297
01298
01299 QPtrList<TrapperDoc> docListNotAlreadyOpen;
01300 docListNotAlreadyOpen.setAutoDelete(true);
01301
01302 open_docs_not_already_open( docListNotAlreadyOpen );
01303
01304 for (TrapperDoc* doc = pDocList->first(); doc != 0; doc = pDocList->next() ) {
01305 doc->importMates(matefile);
01306 }
01307 for (TrapperDoc* doc = docListNotAlreadyOpen.first(); doc != 0; doc = docListNotAlreadyOpen.next() ) {
01308 doc->importMates(matefile);
01309 }
01310
01311
01312 statusBar()->message(tr("Ready."));
01313 }
01314
01315 void TrapperApp::slotTcImport()
01316 {
01317 statusBar()->message(tr("Importing time course data..."));
01318
01319 QString tcfile = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose your time course file to import from");
01320
01321 if (tcfile.isEmpty()) {
01322 return;
01323 }
01324
01325
01326 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01327 if( m ) {
01328 TrapperDoc* doc = m->getDocument();
01329 if ( doc ) {
01330 doc->importTimeCourse(tcfile);
01331 }
01332 }
01333
01334 statusBar()->message(tr("Ready."));
01335
01336 }
01337
01338 void TrapperApp::slotPhdImport()
01339 {
01340 statusBar()->message(tr("Importing phd data..."));
01341
01342 QString phdDirName = QFileDialog::getExistingDirectory(projectDir,this,"phd dir selection","Choose phd directory");
01343
01344 if (phdDirName.isEmpty()) {
01345 return;
01346 }
01347
01348
01349
01350 QPtrList<TrapperDoc> docListNotAlreadyOpen;
01351 docListNotAlreadyOpen.setAutoDelete(true);
01352
01353 open_docs_not_already_open( docListNotAlreadyOpen );
01354
01355 for (TrapperDoc* doc = pDocList->first(); doc != 0; doc = pDocList->next() ) {
01356 doc->importPhd(phdDirName);
01357 }
01358 for (TrapperDoc* doc = docListNotAlreadyOpen.first(); doc != 0; doc = docListNotAlreadyOpen.next() ) {
01359 doc->importPhd(phdDirName);
01360 }
01361
01362
01363
01364 statusBar()->message(tr("Ready."));
01365 }
01366
01367 void TrapperApp::open_docs_not_already_open(QPtrList<TrapperDoc>& notOpenBefore)
01368 {
01369
01370 TrapperDoc* doc;
01371 set<QString> alreadyOpen;
01372
01373 for(doc=pDocList->first(); doc !=0; doc=pDocList->next()) {
01374
01375 alreadyOpen.insert(doc->pathName().section('/', -2));
01376 }
01377
01378
01379 QStringList contigs = contigNamesInProjectDir();
01380
01381 for ( QStringList::Iterator it = contigs.begin(); it != contigs.end(); ++it ) {
01382
01383
01384 if ( *it != "." && *it != ".." && alreadyOpen.find( *it ) == alreadyOpen.end() ) {
01385
01386
01387 TrapperDoc* tdoc = new TrapperDoc(dbenv);
01388 tdoc->newDocument();
01389 if ( !tdoc->openDocument(projectDir + "/" + *it ) ) {
01390 QMessageBox::critical(this, tr("Error !"),tr("Could not open document!"));
01391 delete tdoc;
01392 }
01393 else {
01394 notOpenBefore.append( tdoc );
01395 }
01396
01397 }
01398
01399
01400 }
01401
01402 }
01403
01404
01405
01406
01407
01408
01409
01410
01411
01412
01413
01414
01415
01416
01417
01418
01419
01420
01421
01422
01423
01424
01425
01426
01427
01428
01429
01430 void TrapperApp::slotExport()
01431 {
01432 statusBar()->message(tr("Exporting data to an xml file..."));
01433 QString fn = QFileDialog::getSaveFileName(0, "Trapper Xml (*.xml)", this,
01434 "export to file dialog",
01435 "Choose a filename to save the export data under");
01436 if (fn.isEmpty())
01437 {
01438 return;
01439 }
01440 if ( QFile::exists( fn ) &&
01441 QMessageBox::question(
01442 0,
01443 tr("Overwrite File? -- Trapper"),
01444 tr("A file called %1 already exists."
01445 "Do you want to overwrite it?")
01446 .arg( fn ),
01447 tr("&Yes"), tr("&No"),
01448 QString::null, 0, 1 ) ) {
01449
01450 return;
01451 }
01452
01453 exportToFile(fn);
01454 statusBar()->message(tr("Ready."));
01455 }
01456
01457 void TrapperApp::exportToFile(QString toXmlFile)
01458 {
01459 statusBar()->message(tr("Exporting contig to file..."));
01460
01461
01462
01463 ofstream outFile(toXmlFile.ascii());
01464
01465
01466 outFile<<"<TRAPPER>\n";
01467
01468
01469
01470
01471
01472
01473
01474
01475
01476
01477
01478
01479
01480
01481
01482 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01483 if( m ) {
01484 TrapperDoc* doc = m->getDocument();
01485 if ( doc ) {
01486 doc->saveExport(outFile);
01487 }
01488 }
01489
01490
01491 outFile<<"</TRAPPER>\n";
01492
01493 outFile.close();
01494 statusBar()->message(tr("Ready."));
01495
01496 }
01497
01498 void TrapperApp::setDbHomeDir(QString dir)
01499 {
01500 QDir d(dir);
01501 if ( d.exists() )
01502 {
01503 projectDir = d.absPath();
01504 int ret;
01505
01506 if ((ret = dbenv->open(projectDir, DB_CREATE |
01507 DB_INIT_LOG | DB_INIT_LOCK | DB_INIT_MPOOL | DB_INIT_TXN | DB_RECOVER , 0)) != 0) {
01508 dbenv->err(ret, "environment open: %s", dir.ascii());
01509 exit( 1);
01510 }
01511
01512 }
01513 else
01514 {
01515 QMessageBox::critical( 0,
01516 tr( "Critical Error" ),
01517 tr( "Db home dir \"%1\" doesn't exit" ).arg( dir ) );
01518
01519
01520 exit(1);
01521 }
01522
01523 }
01524
01525 QStringList TrapperApp::contigNamesInProjectDir()
01526 {
01527 QString contigName;
01528 QDir d( projectDir );
01529 Q_ASSERT( d.exists() );
01530 d.setFilter( QDir::Dirs | QDir::NoSymLinks );
01531 d.setSorting( QDir::Name );
01532 QStringList slist = d.entryList();
01533 return slist;
01534 }
01535
01536 void TrapperApp::slotShowStatistics()
01537 {
01538 statusBar()->message(tr("Opening statistics window ..."));
01539
01540 TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
01541 if( m )
01542 {
01543 TrapperDoc* doc = m->getDocument();
01544 if ( doc )
01545 {
01546 QString statisticsText = doc->getStatistics();
01547 QTextEdit * statView = new QTextEdit( );
01548 statView->setReadOnly( true );
01549 statView->setText( statisticsText );
01550 statView->show();
01551 }
01552 }
01553 statusBar()->message(tr("Ready."));
01554 }
01555
01556 void TrapperApp::slotConfigureViewModes()
01557 {
01558 ShowModesDlg * dlg = new ShowModesDlg( this, QString::null );
01559
01560 if ( dlg->exec() == QDialog::Accepted )
01561 {}
01562 }
01563
01564
01565 void TrapperApp::setViewModeConfFile( QString filename )
01566 {
01567 viewmodefile.setName( filename );
01568
01569 if ( ! viewmodefile.open( IO_ReadWrite ) )
01570 {
01571 QMessageBox::critical( 0,
01572 tr( "Critical Error" ),
01573 tr( "Cannot open configuration file %1" ).arg( filename ) );
01574
01575
01576 exit(1);
01577 }
01578
01579 TrapperConf * conf = TrapperConf::instance();
01580 Q_CHECK_PTR( conf );
01581 conf->loadDom( &viewmodefile );
01582 }
01583
01584 void TrapperApp::scroll(int dx, int dy)
01585 {
01586
01587 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01588 if ( m ) m->scrollBy(dx, dy);
01589 }
01590 void TrapperApp::slotNormalMode()
01591 {
01592
01593 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01594 if ( m ) m->setDragMode(false);
01595
01596 }
01597
01598
01599 void TrapperApp::slotDragMode()
01600 {
01601 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01602 if ( m ) m->setDragMode(true);
01603
01604 }
01605
01606 void TrapperApp::slotActivatedWindow(QWidget* w)
01607 {
01608 TrapperView* m = (TrapperView*) w;
01609 if ( m ) {
01610 m->setDragMode(dragModeAction->isOn());
01611 m->setViewTimeCourse(timecourseAction->isOn());
01612 m->setNormalizeTimeCourse(normalizeAction->isOn());
01613 m->setClusterWindow(clusterWindowBox->value());
01614 m->setClusterMinNum(clusterMinNumBox->value());
01615 }
01616
01617 }
01618
01619 void TrapperApp::slotViewTimeCourse(bool toggle)
01620 {
01621 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01622 if ( m ) m->setViewTimeCourse(toggle);
01623
01624 }
01625
01626 void TrapperApp::slotNormalizeTimeCourse(bool toggle)
01627 {
01628 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01629 if ( m ) m->setNormalizeTimeCourse(toggle);
01630
01631 }
01632
01633 void TrapperApp::slotScrollForward()
01634 {
01635 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01636 if ( m ) m->scrollToNextCluster(true);
01637
01638 }
01639
01640 void TrapperApp::slotScrollBackwards()
01641 {
01642 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01643 if ( m ) m->scrollToNextCluster(false);
01644
01645 }
01646
01647 void TrapperApp::slotClusterWindowChanged(int window_size)
01648 {
01649 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01650 if ( m ) m->setClusterWindow(window_size);
01651 }
01652
01653 void TrapperApp::slotClusterNumChanged(int num)
01654 {
01655 TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
01656 if ( m ) m->setClusterMinNum(num);
01657 }
01658
