X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=366a36de498c8d82bee73ec5c72fc78bebd869ca;hb=ea65828ca48c415700ebd130219c875b2e389dff;hp=af24c9ff5c60b9b66c5a906a911109a874c172fb;hpb=df7880a58e6b16d65f9ed8dbe4433efffbe8abec;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index af24c9f..366a36d 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -81,9 +81,7 @@ public class AlignmentPanel extends GAlignmentPanel annotationPanel = new AnnotationPanel(this); alabels = new AnnotationLabels(this); - annotationSpaceFillerHolder.setPreferredSize(annotationPanel. - getPreferredSize()); - annotationScroller.setPreferredSize(annotationPanel.getPreferredSize()); + annotationScroller.setViewportView(annotationPanel); annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); @@ -94,11 +92,8 @@ public class AlignmentPanel extends GAlignmentPanel setScrollValues(0, 0); - annotationPanel.adjustPanelHeight(); - annotationSpaceFillerHolder.setPreferredSize(annotationPanel. - getPreferredSize()); - annotationScroller.setPreferredSize(annotationPanel. - getPreferredSize()); + adjustAnnotationHeight(); + setAnnotationVisible(av.getShowAnnotation()); hscroll.addAdjustmentListener(this); @@ -108,35 +103,171 @@ public class AlignmentPanel extends GAlignmentPanel { public void keyPressed(KeyEvent evt) { + if(av.cursorMode + && evt.getKeyCode()>=KeyEvent.VK_0 + && evt.getKeyCode()<=KeyEvent.VK_9) + { + seqPanel.numberPressed(evt.getKeyChar()); + } + switch (evt.getKeyCode()) { case 27: // escape key - av.setSelectionGroup(null); - repaint(); + alignFrame.deselectAllSequenceMenuItem_actionPerformed(null); break; case KeyEvent.VK_DOWN: - alignFrame.moveSelectedSequences(false); - + if(av.cursorMode) + { + seqPanel.moveCursor(0,1); + } + else + alignFrame.moveSelectedSequences(false); break; case KeyEvent.VK_UP: - alignFrame.moveSelectedSequences(true); + if (av.cursorMode) + { + seqPanel.moveCursor(0,-1); + } + else + alignFrame.moveSelectedSequences(true); + break; + case KeyEvent.VK_LEFT: + if(av.cursorMode) + { + seqPanel.moveCursor(-1,0); + } + break; + + case KeyEvent.VK_RIGHT: + if (av.cursorMode) + { + seqPanel.moveCursor(1,0); + } + break; + + case KeyEvent.VK_SPACE: + if(av.cursorMode) + { + seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown()); + } break; - case KeyEvent.VK_BACK_SPACE: case KeyEvent.VK_DELETE: - alignFrame.cut_actionPerformed(null); + case KeyEvent.VK_BACK_SPACE: + if(!av.cursorMode) + { + alignFrame.cut_actionPerformed(null); + } + else + seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown()); + break; + case KeyEvent.VK_S: + if(av.cursorMode) + { + seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_C: + if(av.cursorMode && !evt.isControlDown()) + { + seqPanel.setCursorColumn(); + } + break; case KeyEvent.VK_P: - seqPanel.seqCanvas.increaseAARatio(); + if(av.cursorMode) + { + seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if(av.cursorMode) + { + seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if(av.cursorMode) + { + seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if(av.cursorMode) + { + seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + av.cursorMode = ! av.cursorMode; + alignFrame.statusBar.setText("Keyboard editing mode is "+ + (av.cursorMode ? "on" : "off")); + if(av.cursorMode) + { + seqPanel.seqCanvas.cursorX = av.startRes; + seqPanel.seqCanvas.cursorY = av.startSeq; + } + seqPanel.seqCanvas.repaint(); + break; + + case KeyEvent.VK_F1: + try + { + ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); + java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); + javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); + + javax.help.HelpBroker hb = hs.createHelpBroker(); + hb.setCurrentID("home"); + hb.setDisplayed(true); + } + catch (Exception ex) + { + ex.printStackTrace(); + } break; - case KeyEvent.VK_L: - seqPanel.seqCanvas.decreaseAARation(); + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + + boolean hide = false; + + SequenceGroup sg = av.getSelectionGroup(); + if(toggleSeqs) + { + if(sg != null && sg.getSize(false) != av.alignment.getHeight()) + { + alignFrame.hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && av.colSel.getSelected().size() > 0)) + alignFrame.showAllSeqs_actionPerformed(null); + } + + if (toggleCols) + { + if(av.colSel.getSelected().size() > 0) + { + alignFrame.hideSelColumns_actionPerformed(null); + if(!toggleSeqs) + av.selectionGroup = sg; + } + else if(!hide) + alignFrame.showAllColumns_actionPerformed(null); + } break; + } + } } }); @@ -242,26 +373,43 @@ public class AlignmentPanel extends GAlignmentPanel * * @param results DOCUMENT ME! */ - public void highlightSearchResults(int[] results) + public void highlightSearchResults(SearchResults results) { seqPanel.seqCanvas.highlightSearchResults(results); // do we need to scroll the panel? if (results != null) { - SequenceI seq = av.alignment.getSequenceAt(results[0]); - int start = seq.findIndex(results[1]) - 1; - int end = seq.findIndex(results[2]) - 1; + SequenceI seq = results.getResultSequence(0); + int seqIndex = av.alignment.findIndex(seq); + int start = seq.findIndex(results.getResultStart(0)) - 1; + int end = seq.findIndex(results.getResultEnd(0)) - 1; - if ( (av.getStartRes() > start) || (av.getEndRes() < end) || - ( (av.getStartSeq() > results[0]) || - (av.getEndSeq() < results[0]))) + if(!av.wrapAlignment) { - setScrollValues(start, results[0]); + if ( (av.getStartRes() > end) || (av.getEndRes() < start) || + ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + { + setScrollValues(start, seqIndex); + } + } + else + { + scrollToWrappedVisible(start); } } } + void scrollToWrappedVisible(int res) + { + int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) ) + { + vscroll.setValue(res / cwidth); + av.startRes = vscroll.getValue() * cwidth; + } + } + /** * DOCUMENT ME! * @@ -297,6 +445,38 @@ public class AlignmentPanel extends GAlignmentPanel repaint(); } + public void adjustAnnotationHeight() + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + while(alignFrame.getHeight()==0) + { + Thread.yield(); + } + + int height = annotationPanel.adjustPanelHeight(); + + if (height > alignFrame.getHeight() / 2) + { + height = alignFrame.getHeight() / 2; + } + + annotationScroller.setPreferredSize( + new Dimension(annotationScroller.getWidth(), + height)); + + annotationSpaceFillerHolder.setPreferredSize(new Dimension( + annotationSpaceFillerHolder.getWidth(), + height)); + + annotationPanel.repaint(); + repaint(); + } + }); + } + /** * DOCUMENT ME! * @@ -363,7 +543,7 @@ public class AlignmentPanel extends GAlignmentPanel */ public boolean scrollRight(boolean right) { - if (right) + if (!right) { if (hscroll.getValue() < 1) { @@ -397,30 +577,36 @@ public class AlignmentPanel extends GAlignmentPanel */ public void setScrollValues(int x, int y) { - av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - - 1); + + int width = av.alignment.getWidth(); + int height = av.alignment.getHeight(); + + if(av.hasHiddenColumns) + width = av.getColumnSelection().findColumnPosition(width); + + av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1); hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; - if (hextent > av.alignment.getWidth()) + if (hextent > width) { - hextent = av.alignment.getWidth(); + hextent = width; } - if (vextent > av.alignment.getHeight()) + if (vextent > height) { - vextent = av.alignment.getHeight(); + vextent = height; } - if ( (hextent + x) > av.getAlignment().getWidth()) + if ( (hextent + x) > width) { - x = av.getAlignment().getWidth() - hextent; + x = width - hextent; } - if ( (vextent + y) > av.getAlignment().getHeight()) + if ( (vextent + y) > height) { - y = av.getAlignment().getHeight() - vextent; + y = height - vextent; } if (y < 0) @@ -433,8 +619,8 @@ public class AlignmentPanel extends GAlignmentPanel x = 0; } - hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); - vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); } /** @@ -462,10 +648,26 @@ public class AlignmentPanel extends GAlignmentPanel if (av.getWrapAlignment()) { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); - av.setStartRes(vscroll.getValue() * rowSize); - av.setEndRes( (vscroll.getValue() + 1) * rowSize); + if(offy>-1) + { + int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. + seqCanvas.getWidth()); + av.setStartRes(offy * rowSize); + av.setEndRes( (offy + 1) * rowSize); + } + else + { + //This is only called if file loaded is a jar file that + //was wrapped when saved and user has wrap alignment true + //as preference setting + SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + setScrollValues(av.getStartRes(), av.getStartSeq()); + } + }); + } } else { @@ -480,28 +682,33 @@ public class AlignmentPanel extends GAlignmentPanel overviewPanel.setBoxPosition(); } - int xShift = av.getStartRes() - oldX; - int yShift = av.getStartSeq() - oldY; + int scrollX = av.startRes - oldX; + int scrollY = av.startSeq - oldY; - if ( (xShift != 0 && yShift != 0) || - (Math.abs(xShift) > av.getEndRes() - av.getStartRes() - || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq()) - || av.getWrapAlignment() - || !fastPaint) + if (av.getWrapAlignment() || !fastPaint) { - // Either no shift at all, or shift greater than visible amount repaint(); } else { - idPanel.idCanvas.fastPaint(yShift); - seqPanel.seqCanvas.fastPaint(xShift, yShift); - - scalePanel.repaint(); - - if (av.getShowAnnotation()) + // Make sure we're not trying to draw a panel + // larger than the visible window + if(scrollX>av.endRes-av.startRes) + scrollX = av.endRes-av.startRes; + else if(scrollX 0 ? idPanel.getWidth() : + calculateIdWidth().width + 4; + } + void makeAlignmentImage(int type, File file) { - int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; - int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth); + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); - if (idPanel.getWidth() == 0) - { - width += calculateIdWidth().getWidth() + 4; - } + int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; + int width = getVisibleIdWidth() + (maxwidth * av.charWidth); if (av.getWrapAlignment()) { height = getWrappedHeight(); - width = seqPanel.getWidth() + idPanel.getWidth(); + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + width = alignFrame.getWidth() - 22; + } + else + width = seqPanel.getWidth() + getVisibleIdWidth(); + } else if (av.getShowAnnotation()) { @@ -841,15 +1078,19 @@ public class AlignmentPanel extends GAlignmentPanel if (av.getWrapAlignment()) { if(im.getGraphics()!=null) + { printWrappedAlignment(im.getGraphics(), width, height, 0); + im.writeImage(); + } } else { if(im.getGraphics()!=null) + { printUnwrapped(im.getGraphics(), width, height, 0); + im.writeImage(); + } } - - im.writeImage(); } catch (OutOfMemoryError err) { @@ -892,7 +1133,7 @@ public class AlignmentPanel extends GAlignmentPanel { ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS ////////////////////////////////////////////// - int idWidth = calculateIdWidth().width + 4; + int idWidth = getVisibleIdWidth(); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -916,7 +1157,7 @@ public class AlignmentPanel extends GAlignmentPanel sy = s * av.charHeight + scaleHeight; SequenceI seq = av.alignment.getSequenceAt(s); - java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures(); + SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures(); SequenceGroup[] groups = av.alignment.findAllGroups(seq); for(res =0; res= seq.findPosition(res))) + if ( (features[f].getBegin() <= seq.findPosition(res)) && + (features[f].getEnd() >= seq.findPosition(res))) { - if (sf.getType().equals("disulfide bond")) + if (features[f].getType().equals("disulfide bond")) { - if (sf.getBegin() == seq.findPosition(res) - || sf.getEnd() == seq.findPosition(res)) + if (features[f].getBegin() == seq.findPosition(res) + || features[f].getEnd() == seq.findPosition(res)) { - text.append("
disulfide bond " + sf.getBegin() + ":" + - sf.getEnd()); + text.append("
disulfide bond " + features[f].getBegin() + ":" + + features[f].getEnd()); } } else { text.append("
"); - text.append(sf.getType()); - if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription())) - text.append(" " + sf.getDescription()); + text.append(features[f].getType()); + if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription())) + text.append(" " + features[f].getDescription()); - if (sf.getStatus() != null && sf.getStatus().length()>0) + if (features[f].getValue("status") != null ) { - text.append(" (" + sf.getStatus() + ")"); + text.append(" (" + features[f].getValue("status") + ")"); } } } @@ -1017,9 +1257,18 @@ public class AlignmentPanel extends GAlignmentPanel int getWrappedHeight() { + int seqPanelWidth = seqPanel.seqCanvas.getWidth(); + + //If headless, seqPanel will have 0 width + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth(); + } int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth( - seqPanel.seqCanvas.getWidth()); + seqPanelWidth + ); int hgap = av.charHeight; if (av.scaleAboveWrapped) @@ -1035,7 +1284,12 @@ public class AlignmentPanel extends GAlignmentPanel + hgap + annotationHeight; - int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight; + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + + + int height = ( (maxwidth / chunkWidth) + 1) * cHeight; return height; }