X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=7984991493213e2ec273905968792d4bd9af4626;hb=0039639a8b6fa7a9bfc131c83a493b5a696f0104;hp=c1d383ef2b81e6f17f72c577f3534907e924386c;hpb=96589f3091facee1b50db52995b3a13425f0e96b;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index c1d383e..7984991 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -68,6 +68,17 @@ public class AlignFrame { viewport = new AlignViewport(al); + if(viewport.vconsensus==null) + { + //Out of memory caluclating consensus. + BLOSUM62Colour.setEnabled(false); + PIDColour.setEnabled(false); + conservationMenuItem.setEnabled(false); + modifyConservation.setEnabled(false); + abovePIDThreshold.setEnabled(false); + modifyPID.setEnabled(false); + } + alignPanel = new AlignmentPanel(this, viewport); alignPanel.annotationPanel.adjustPanelHeight(); alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel. @@ -76,32 +87,36 @@ public class AlignFrame getPreferredSize()); alignPanel.setAnnotationVisible(viewport.getShowAnnotation()); + String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); + + if(sortby.equals("Id")) + sortIDMenuItem_actionPerformed(null); + else if(sortby.equals("Pairwise Identity")) + sortPairwiseMenuItem_actionPerformed(null); + getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); - addInternalFrameListener(new InternalFrameAdapter() + viewport.addPropertyChangeListener(new PropertyChangeListener() { - public void internalFrameActivated(InternalFrameEvent evt) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - alignPanel.requestFocus(); - } - }); - } - }); + public void propertyChange(PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) + { + alignmentChanged(); + } + } + }); + + addServiceListeners(); } /* Set up intrinsic listeners for dynamically generated GUI bits. */ private void addServiceListeners() { - - final AlignFrame thisFrame = this; final java.beans.PropertyChangeListener thisListener; // Do this once to get current state - thisFrame.BuildWebServiceMenu(); + BuildWebServiceMenu(); Desktop.discoverer.addPropertyChangeListener( thisListener = new java.beans.PropertyChangeListener() { @@ -111,7 +126,7 @@ public class AlignFrame if (evt.getPropertyName().equals("services")) { // System.out.println("Rebuilding web service menu"); - thisFrame.BuildWebServiceMenu(); + BuildWebServiceMenu(); } } }); @@ -123,6 +138,7 @@ public class AlignFrame { // System.out.println("deregistering discoverer listener"); Desktop.discoverer.removePropertyChangeListener(thisListener); + closeMenuItem_actionPerformed(null); } ; }); @@ -264,7 +280,8 @@ public class AlignFrame { java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(file)); - out.println(output); + + out.print(output); out.close(); return true; } @@ -348,6 +365,7 @@ public class AlignFrame { try { + PaintRefresher.components.remove(viewport.alignment); this.setClosed(true); } catch (Exception ex) @@ -409,6 +427,7 @@ public class AlignFrame redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE)); restoreHistoryItem(hi); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** @@ -421,9 +440,7 @@ public class AlignFrame HistoryItem hi = (HistoryItem) redoList.pop(); restoreHistoryItem(hi); updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } // used by undo and redo @@ -468,9 +485,6 @@ public class AlignFrame updateEditMenuBar(); - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } @@ -699,20 +713,17 @@ public class AlignFrame } else { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } catch (Exception ex) { + // could be anything being pasted in here } - // could be anything being pasted in here + } /** @@ -733,7 +744,6 @@ public class AlignFrame */ protected void delete_actionPerformed(ActionEvent e) { - boolean seqsdeleted = false; if (viewport.getSelectionGroup() == null) { @@ -765,7 +775,6 @@ public class AlignFrame if (seq.getSequence().length() < 1) { - seqsdeleted = true; viewport.getAlignment().deleteSequence(seq); } else @@ -777,13 +786,10 @@ public class AlignFrame viewport.setSelectionGroup(null); viewport.alignment.deleteGroup(sg); - if (seqsdeleted) - { - viewport.firePropertyChange("alignment", null, + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight()); + if (viewport.getAlignment().getHeight() < 1) { @@ -795,10 +801,6 @@ public class AlignFrame { } } - - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); } /** @@ -907,7 +909,7 @@ public class AlignFrame } } - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } @@ -945,7 +947,7 @@ public class AlignFrame } } - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } @@ -959,10 +961,16 @@ public class AlignFrame addHistoryItem(new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + viewport.getAlignment().removeGaps(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + + viewport.setStartRes(seq.findIndex(startRes)-1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** @@ -975,6 +983,12 @@ public class AlignFrame addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + SequenceI current; int jSize; @@ -989,7 +1003,7 @@ public class AlignFrame { seqs = viewport.getSelectionGroup().sequences; start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); + end = viewport.getSelectionGroup().getEndRes()+1; } else { @@ -1001,24 +1015,103 @@ public class AlignFrame current = (SequenceI) seqs.elementAt(i); jSize = current.getLength(); + // Removing a range is much quicker than removing gaps + // one by one for long sequences int j = start; + int rangeStart=-1, rangeEnd=-1; do { if (jalview.util.Comparison.isGap(current.getCharAt(j))) { - current.deleteCharAt(j); - j--; - jSize--; + if(rangeStart==-1) + { + rangeStart = j; + rangeEnd = j+1; + } + else + { + rangeEnd++; + } + j++; + } + else + { + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); + j-=rangeEnd-rangeStart; + jSize-=rangeEnd-rangeStart; + rangeStart = -1; + rangeEnd = -1; + } + else + j++; } - j++; } while (j < end && j < jSize); + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); + } } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.setStartRes(seq.findIndex(startRes)-1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + public void alignmentChanged() + { + if(viewport.vconsensus!=null) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); + + alignPanel.repaint(); + } + + void resetAllColourSchemes() + { + ColourSchemeI cs = viewport.globalColourScheme; + if(cs!=null) + { + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). + resetClustalX(viewport.alignment.getSequences(), + viewport.alignment.getWidth()); + } + + cs.setConsensus(viewport.vconsensus); + if (cs.conservationApplied()) + { + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + + cs.setConservation(c); + } + } + + int s, sSize = viewport.alignment.getGroups().size(); + for(s=0; s