X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=65923997ff9dd8c30baf65227fd87a8059db8e71;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=93f48ee3ae1254fb7d28c5021631609bcbd56bfa;hpb=c23f28e21e50f93f6e695bdc86247f2700c35869;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 93f48ee..6592399 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -38,7 +38,8 @@ public class AlignFrame extends Frame implements ActionListener, public AlignViewport viewport; int NEW_WINDOW_WIDTH = 700; int NEW_WINDOW_HEIGHT = 500; - jalview.bin.JalviewLite applet; + + String jalviewServletURL; public AlignFrame(AlignmentI al, @@ -46,6 +47,9 @@ public class AlignFrame extends Frame implements ActionListener, String title, boolean embedded) { + + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + try{ jbInit(); }catch(Exception ex) @@ -53,7 +57,6 @@ public class AlignFrame extends Frame implements ActionListener, ex.printStackTrace(); } - this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); @@ -369,117 +372,146 @@ public void itemStateChanged(ItemEvent evt) } public void actionPerformed(ActionEvent evt) { - if(evt.getSource()==inputText) + Object source = evt.getSource(); + + if(source==inputText) inputText_actionPerformed(); - else if(evt.getSource()==loadTree) + else if(source==loadTree) loadTree_actionPerformed(); - else if(evt.getSource()==loadApplication) + else if(source==loadApplication) launchFullApplication(); - else if(evt.getSource()==closeMenuItem) + else if(source==closeMenuItem) closeMenuItem_actionPerformed(); - else if(evt.getSource()==copy) + else if(source==copy) copy_actionPerformed(); - else if(evt.getSource()==undoMenuItem) + else if(source==undoMenuItem) undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) + else if(source==redoMenuItem) redoMenuItem_actionPerformed(); - else if(evt.getSource()==inputText) + else if(source==inputText) inputText_actionPerformed(); - else if(evt.getSource()==closeMenuItem) + else if(source==closeMenuItem) closeMenuItem_actionPerformed(); - else if(evt.getSource()==undoMenuItem) + else if(source==undoMenuItem) undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) + else if(source==redoMenuItem) redoMenuItem_actionPerformed(); - else if(evt.getSource()==copy) + else if(source==copy) copy_actionPerformed(); - else if(evt.getSource()==pasteNew) + else if(source==pasteNew) pasteNew_actionPerformed(); - else if(evt.getSource()==pasteThis) + else if(source==pasteThis) pasteThis_actionPerformed(); - else if(evt.getSource()==cut) + else if(source==cut) cut_actionPerformed(); - else if(evt.getSource()==delete) + else if(source==delete) delete_actionPerformed(); - else if(evt.getSource()==deleteGroups) + else if(source==deleteGroups) deleteGroups_actionPerformed(); - else if(evt.getSource()==selectAllSequenceMenuItem) + else if(source==selectAllSequenceMenuItem) selectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==deselectAllSequenceMenuItem) + else if(source==deselectAllSequenceMenuItem) deselectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==invertSequenceMenuItem) + else if(source==invertSequenceMenuItem) invertSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==remove2LeftMenuItem) + else if(source==invertColSel) + { viewport.invertColumnSelection(); repaint(); } + else if(source==remove2LeftMenuItem) remove2LeftMenuItem_actionPerformed(); - else if(evt.getSource()==remove2RightMenuItem) + else if(source==remove2RightMenuItem) remove2RightMenuItem_actionPerformed(); - else if(evt.getSource()==removeGappedColumnMenuItem) + else if(source==removeGappedColumnMenuItem) removeGappedColumnMenuItem_actionPerformed(); - else if(evt.getSource()==removeAllGapsMenuItem) + else if(source==removeAllGapsMenuItem) removeAllGapsMenuItem_actionPerformed(); - else if(evt.getSource()==findMenuItem) + else if(source==findMenuItem) findMenuItem_actionPerformed(); - else if(evt.getSource()==font) + else if(source==font) font_actionPerformed(); - else if(evt.getSource()==featureSettings) + else if(source==showColumns) + { + viewport.showAllHiddenColumns(); repaint(); + } + else if(source==showSeqs) + { + viewport.showAllHiddenSeqs(); repaint(); + } + else if(source == hideColumns) + { + viewport.hideSelectedColumns(); repaint(); + } + else if(source == hideSequences && viewport.getSelectionGroup()!=null) + { + SequenceI[] seqs = viewport.getSelectionGroup().getSequencesInOrder( + viewport.alignment + ); + + for (int i = 0; i < seqs.length; i++) + { + viewport.hideSequence(seqs[i]); + } + + alignPanel.repaint(); + } + else if(source==featureSettings) featureSettings_actionPerformed(); - else if(evt.getSource()==overviewMenuItem) + else if(source==overviewMenuItem) overviewMenuItem_actionPerformed(); - else if(evt.getSource()==noColourmenuItem) + else if(source==noColourmenuItem) noColourmenuItem_actionPerformed(); - else if(evt.getSource()==clustalColour) + else if(source==clustalColour) clustalColour_actionPerformed(); - else if(evt.getSource()==zappoColour) + else if(source==zappoColour) zappoColour_actionPerformed(); - else if(evt.getSource()==taylorColour) + else if(source==taylorColour) taylorColour_actionPerformed(); - else if(evt.getSource()==hydrophobicityColour) + else if(source==hydrophobicityColour) hydrophobicityColour_actionPerformed(); - else if(evt.getSource()==helixColour) + else if(source==helixColour) helixColour_actionPerformed(); - else if(evt.getSource()==strandColour) + else if(source==strandColour) strandColour_actionPerformed(); - else if(evt.getSource()==turnColour) + else if(source==turnColour) turnColour_actionPerformed(); - else if(evt.getSource()==buriedColour) + else if(source==buriedColour) buriedColour_actionPerformed(); - else if(evt.getSource()==nucleotideColour) + else if(source==nucleotideColour) nucleotideColour_actionPerformed(); - else if(evt.getSource()==modifyPID) + else if(source==modifyPID) modifyPID_actionPerformed(); - else if(evt.getSource()==modifyConservation) + else if(source==modifyConservation) modifyConservation_actionPerformed(); - else if(evt.getSource()==userDefinedColour) + else if(source==userDefinedColour) userDefinedColour_actionPerformed(); - else if(evt.getSource()==PIDColour) + else if(source==PIDColour) PIDColour_actionPerformed(); - else if(evt.getSource()==BLOSUM62Colour) + else if(source==BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); - else if(evt.getSource()==annotationColour) + else if(source==annotationColour) new AnnotationColourChooser(viewport, alignPanel); - else if(evt.getSource()==sortPairwiseMenuItem) + else if(source==sortPairwiseMenuItem) sortPairwiseMenuItem_actionPerformed(); - else if(evt.getSource()==sortIDMenuItem) + else if(source==sortIDMenuItem) sortIDMenuItem_actionPerformed(); - else if(evt.getSource()==sortGroupMenuItem) + else if(source==sortGroupMenuItem) sortGroupMenuItem_actionPerformed(); - else if(evt.getSource()==removeRedundancyMenuItem) + else if(source==removeRedundancyMenuItem) removeRedundancyMenuItem_actionPerformed(); - else if(evt.getSource()==pairwiseAlignmentMenuItem) + else if(source==pairwiseAlignmentMenuItem) pairwiseAlignmentMenuItem_actionPerformed(); - else if(evt.getSource()==PCAMenuItem) + else if(source==PCAMenuItem) PCAMenuItem_actionPerformed(); - else if(evt.getSource()==averageDistanceTreeMenuItem) + else if(source==averageDistanceTreeMenuItem) averageDistanceTreeMenuItem_actionPerformed(); - else if(evt.getSource()==neighbourTreeMenuItem) + else if(source==neighbourTreeMenuItem) neighbourTreeMenuItem_actionPerformed(); - else if(evt.getSource()==njTreeBlosumMenuItem) + else if(source==njTreeBlosumMenuItem) njTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==avDistanceTreeBlosumMenuItem) + else if(source==avDistanceTreeBlosumMenuItem) avTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==documentation) + else if(source==documentation) documentation_actionPerformed(); - else if(evt.getSource()==about) + else if(source==about) about_actionPerformed(); } @@ -507,28 +539,34 @@ public void itemStateChanged(ItemEvent evt) void launchFullApplication() { - StringBuffer url = new StringBuffer("http://bug.compbio.dundee.ac.uk:8080/Jalview/jalview?"); + StringBuffer url = new StringBuffer(jalviewServletURL); - url.append("open="+ - appendProtocol( applet.getParameter("file") ) ); + url.append("?open="+ + appendProtocol( viewport.applet.getParameter("file") ) ); - if(applet.getParameter("features")!=null) + if(viewport.applet.getParameter("features")!=null) { url.append( "&features=" ); - url.append( appendProtocol( applet.getParameter("features") ) ); + url.append( appendProtocol( viewport.applet.getParameter("features") ) ); } - if(applet.getParameter("defaultColour")!=null) + if(viewport.applet.getParameter("annotations")!=null) + { + url.append( "&annotations=" ); + url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); + } + + if(viewport.applet.getParameter("defaultColour")!=null) { url.append("&colour=" + - removeWhiteSpace(applet.getParameter("defaultColour")) + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) ); } - if(applet.getParameter("userDefinedColour")!=null) + if(viewport.applet.getParameter("userDefinedColour")!=null) { url.append( "&colour=" + - removeWhiteSpace( applet.getParameter("userDefinedColour") ) + removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) ); } @@ -557,7 +595,7 @@ public void itemStateChanged(ItemEvent evt) new URL(url); }catch(java.net.MalformedURLException ex) { - url = applet.getCodeBase()+url; + url = viewport.applet.getCodeBase()+url; } return url; } @@ -565,7 +603,7 @@ public void itemStateChanged(ItemEvent evt) public void closeMenuItem_actionPerformed() { PaintRefresher.components.remove(viewport.alignment); - if(PaintRefresher.components.size()==0 && applet==null) + if(PaintRefresher.components.size()==0 && viewport.applet==null) System.exit(0); this.dispose(); @@ -647,13 +685,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(false).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(false).contains(temp)) { continue; } @@ -667,13 +705,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(true).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(true).contains(temp)) { continue; } @@ -686,7 +724,8 @@ public void itemStateChanged(ItemEvent evt) alignPanel.repaint(); } - StringBuffer copiedSequences; + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) @@ -697,7 +736,7 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); @@ -707,7 +746,26 @@ public void itemStateChanged(ItemEvent evt) int index = 0, startRes, endRes; char ch; - for (int i = 0; i < sg.getSize(); i++) + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + { + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); + i++) + { + int[] region = (int[]) + viewport.getColumnSelection().getHiddenColumns().elementAt(i); + + copiedHiddenColumns.addElement(new int[] + {region[0] - hiddenOffset, + region[1] - hiddenOffset}); + } + } + else + copiedHiddenColumns = null; + + + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = null; @@ -815,9 +873,18 @@ public void itemStateChanged(ItemEvent evt) newtitle = newtitle.concat("- from " + getTitle()); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), - applet, + viewport.applet, newtitle, false); + if (copiedHiddenColumns != null) + { + for (int i = 0; i < copiedHiddenColumns.size(); i++) + { + int[] region = (int[]) copiedHiddenColumns.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); @@ -853,10 +920,10 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = viewport.getSelectionGroup(); boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) + if(sg.getSize(false)==viewport.alignment.getHeight()) allSequences = true; - for (int i = 0; i < sg.sequences.size(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.getAlignment().findIndex(seq); @@ -1037,10 +1104,10 @@ public void itemStateChanged(ItemEvent evt) int start=0, end = viewport.alignment.getWidth(); if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) + && viewport.getSelectionGroup().getSequences(false) != null + && viewport.getSelectionGroup().getSize(false)>0) { - seqs = viewport.getSelectionGroup().sequences; + seqs = viewport.getSelectionGroup().getSequences(true); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes()+1; } @@ -1146,7 +1213,8 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s); if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth()); + ((ClustalxColourScheme)sg.cs).resetClustalX( + sg.getSequences(true), sg.getWidth()); } sg.recalcConservation(); } @@ -1382,7 +1450,7 @@ public void itemStateChanged(ItemEvent evt) } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); } else { @@ -1402,7 +1470,7 @@ public void itemStateChanged(ItemEvent evt) || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth())); } else sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); @@ -1411,7 +1479,7 @@ public void itemStateChanged(ItemEvent evt) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(true), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -1529,7 +1597,7 @@ public void itemStateChanged(ItemEvent evt) public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize() > 1) + if (viewport.getSelectionGroup().getSize(false) > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1559,8 +1627,8 @@ public void itemStateChanged(ItemEvent evt) } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() < 4 && - viewport.getSelectionGroup().getSize() > 0) + viewport.getSelectionGroup().getSize(false) < 4 && + viewport.getSelectionGroup().getSize(false) > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -1618,19 +1686,9 @@ public void itemStateChanged(ItemEvent evt) } - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); - } - else - { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); - } + final TreePanel tp = new TreePanel(viewport, + type, + pwType); addTreeMenuItem(tp, title); @@ -1650,8 +1708,9 @@ public void itemStateChanged(ItemEvent evt) public void loadTree(jalview.io.NewickFile tree, String treeFile) { TreePanel tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), - tree, "From File - ", treeFile); + treeFile, + "From File - ", + tree); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } @@ -1752,7 +1811,7 @@ public void itemStateChanged(ItemEvent evt) public void showURL(String url, String target) { - if (applet == null) + if (viewport.applet == null) { System.out.println("Not running as applet - no browser available."); } @@ -1761,7 +1820,7 @@ public void itemStateChanged(ItemEvent evt) try { System.out.println("Show url: "+url); - applet.getAppletContext().showDocument(new java.net.URL(url), + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), target); } catch (Exception ex) @@ -2044,6 +2103,20 @@ public void itemStateChanged(ItemEvent evt) sequenceFeatures.setState(false); annotationColour.setLabel("by Annotation..."); annotationColour.addActionListener(this); + invertSequenceMenuItem.setLabel("Invert Sequence Selection"); + invertColSel.setLabel("Invert Column Selection"); + menu1.setLabel("Show"); + showColumns.setLabel("All Columns "); + showSeqs.setLabel("All Sequences"); + menu2.setLabel("Hide"); + hideColumns.setLabel("Selected Columns"); + hideSequences.setLabel("Selected Sequences"); + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); @@ -2054,7 +2127,8 @@ public void itemStateChanged(ItemEvent evt) alignFrameMenuBar.add(helpMenu); fileMenu.add(inputText); fileMenu.add(outputTextboxMenu); - // fileMenu.add(loadApplication); + if(jalviewServletURL!=null) + fileMenu.add(loadApplication); fileMenu.addSeparator(); fileMenu.add(loadTree); fileMenu.add(closeMenuItem); @@ -2068,7 +2142,8 @@ public void itemStateChanged(ItemEvent evt) editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); + editMenu.add(invertColSel); + editMenu.add(deleteGroups); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); @@ -2078,13 +2153,15 @@ public void itemStateChanged(ItemEvent evt) searchMenu.add(findMenuItem); viewMenu.add(font); viewMenu.addSeparator(); - viewMenu.add(seqLimits); - viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); viewMenu.addSeparator(); + viewMenu.add(seqLimits); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); viewMenu.add(colourTextMenuItem); @@ -2135,6 +2212,10 @@ public void itemStateChanged(ItemEvent evt) calculate.add(njTreeBlosumMenuItem); helpMenu.add(documentation); helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); } public void setEmbedded() @@ -2187,16 +2268,16 @@ public void itemStateChanged(ItemEvent evt) fileMenu.remove(closeMenuItem); fileMenu.remove(3); // Seperator - applet.setLayout(new BorderLayout()); - applet.add(embeddedMenu, BorderLayout.NORTH); - applet.add(statusBar, BorderLayout.SOUTH); - // applet.validate(); + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + // viewport.applet.validate(); - alignPanel.setSize(applet.size().width, applet.size().height + alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); - applet.add(alignPanel, BorderLayout.CENTER); - applet.validate(); + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); } @@ -2207,6 +2288,13 @@ public void itemStateChanged(ItemEvent evt) MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); public void mousePressed(MouseEvent evt) {