X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=dca9da4a84e744d2f704510390172c8bc4009d25;hb=c97c8a9e4fd58a4927e040e314c5be3c5356745e;hp=abd76d69481f336fa69ba4b5b838868c091489bd;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index abd76d6..dca9da4 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.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 @@ -28,7 +28,7 @@ import jalview.datamodel.*; import jalview.schemes.*; public class APopupMenu - extends java.awt.PopupMenu + extends java.awt.PopupMenu implements ActionListener, ItemListener { Menu groupMenu = new Menu(); protected MenuItem clustalColour = new MenuItem(); @@ -46,15 +46,29 @@ public class APopupMenu MenuItem noColourmenuItem = new MenuItem(); protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - AlignmentPanel ap; + final AlignmentPanel ap; MenuItem unGroupMenuItem = new MenuItem(); MenuItem nucleotideMenuItem = new MenuItem(); Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); CheckboxMenuItem showText = new CheckboxMenuItem(); CheckboxMenuItem showColourText = new CheckboxMenuItem(); - - public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links) + Menu editMenu = new Menu("Edit"); + MenuItem copy = new MenuItem("Copy (Jalview Only)"); + MenuItem cut = new MenuItem("Cut (Jalview Only)"); + MenuItem toUpper = new MenuItem("To Upper Case"); + MenuItem toLower = new MenuItem("To Lower Case"); + MenuItem toggleCase = new MenuItem("Toggle Case"); + Menu outputmenu = new Menu(); + Menu seqMenu = new Menu(); + MenuItem pdb = new MenuItem(); + MenuItem hideSeqs = new MenuItem(); + MenuItem repGroup = new MenuItem(); + + Sequence seq; + MenuItem revealAll = new MenuItem(); + + public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { /////////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -63,7 +77,8 @@ public class APopupMenu // If from the IDPanel, we must display the sequence menu ////////////////////////////////////////////////////////// - this.ap = ap; + this.ap = apanel; + this.seq = seq; try { @@ -74,20 +89,34 @@ public class APopupMenu e.printStackTrace(); } + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + { + MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] ); + + item.addActionListener(this); + outputmenu.add(item); + } + SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + + if (sg != null && sg.getSize(false)>0) { showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); - } + if (!ap.av.alignment.getGroups().contains(sg)) + { + groupMenu.remove(unGroupMenuItem); + } - if (!ap.av.alignment.getGroups().contains(sg)) + } + else { - groupMenu.remove(unGroupMenuItem); + remove(hideSeqs); + remove(groupMenu); } - if (seq != null && links!=null) + if (links!=null) { Menu linkMenu = new Menu("Link"); MenuItem item; @@ -97,92 +126,238 @@ public class APopupMenu link = links.elementAt(i).toString(); final String target = link.substring(0, link.indexOf("|")); item = new MenuItem(target); - final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$")) - + seq.getName() + - link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + final String url; + + if (link.indexOf("$SEQUENCE_ID$") > -1) + { + String id = seq.getName(); + if (id.indexOf("|") > -1) + id = id.substring(id.lastIndexOf("|") + 1); + + url = link.substring(link.indexOf("|") + 1, + link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + } + else + url = link.substring(link.lastIndexOf("|")+1); + + System.out.println("add "+url +" "+target); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - jalview.bin.JalviewLite.showURL(url, target); + ap.alignFrame.showURL(url, target); } }); linkMenu.add(item); } - add(linkMenu); + if(seq!=null) + seqMenu.add(linkMenu); + else + add(linkMenu); } + if(seq!=null) + { + seqMenu.setLabel(seq.getName()); + repGroup.setLabel("Represent Group with " + seq.getName()); + } + else + remove(seqMenu); + + if(!ap.av.hasHiddenRows) + remove(revealAll); } - private void jbInit() - throws Exception + public void itemStateChanged(ItemEvent evt) { - groupMenu.setLabel("Group"); - groupMenu.setLabel("Define"); + if(evt.getSource()==abovePIDColour) + abovePIDColour_itemStateChanged(); + else if(evt.getSource()==showColourText) + showColourText_itemStateChanged(); + else if(evt.getSource()==showText) + showText_itemStateChanged(); + else if(evt.getSource()==showBoxes) + showBoxes_itemStateChanged() ; + } - unGroupMenuItem.setLabel("Remove Group"); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + if(source==clustalColour) + clustalColour_actionPerformed(); + else if(source==zappoColour) + zappoColour_actionPerformed(); + else if(source==taylorColour) + taylorColour_actionPerformed(); + else if(source==hydrophobicityColour) + hydrophobicityColour_actionPerformed(); + else if(source==helixColour) + helixColour_actionPerformed(); + else if(source==strandColour) + strandColour_actionPerformed(); + else if(source==turnColour) + turnColour_actionPerformed(); + else if(source==buriedColour) + buriedColour_actionPerformed(); + else if(source==nucleotideMenuItem) + nucleotideMenuItem_actionPerformed(); + + else if (source == userDefinedColour) + userDefinedColour_actionPerformed(); + else if (source == PIDColour) + PIDColour_actionPerformed(); + else if (source == BLOSUM62Colour) + BLOSUM62Colour_actionPerformed(); + else if (source == noColourmenuItem) + noColourmenuItem_actionPerformed(); + else if (source == conservationMenuItem) + conservationMenuItem_itemStateChanged(); + else if (source == unGroupMenuItem) + unGroupMenuItem_actionPerformed(); + + else if(source == pdb) + addPDB(); + else if(source == hideSeqs) + hideSequences(false); + else if(source == repGroup) + hideSequences(true); + else if(source == revealAll) { - public void actionPerformed(ActionEvent e) - { - unGroupMenuItem_actionPerformed(e); - } - }); + ap.av.showAllHiddenSeqs(); + } - nucleotideMenuItem.setLabel("Nucleotide"); - nucleotideMenuItem.addActionListener(new ActionListener() + else if(source==copy) + ap.alignFrame.copy_actionPerformed(); + else if(source==cut) + ap.alignFrame.cut_actionPerformed(); + else if(source==toUpper || source==toLower || source==toggleCase) { - public void actionPerformed(ActionEvent e) + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) { - nucleotideMenuItem_actionPerformed(e); - } - }); - conservationMenuItem.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - conservationMenuItem_itemStateChanged(itemEvent); + for (int g = 0; g < sg.getSize(true); g++) + { + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do + { + if (ap.av.hasHiddenColumns) + { + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + end = sg.getEndRes() + 1; + if (end > sg.getEndRes()) + end = sg.getEndRes() + 1; + } + + if (source == toggleCase) + ( (SequenceI) sg.getSequences(true).elementAt(g)) + .toggleCase(start, end); + else + ( (SequenceI) sg.getSequences(true).elementAt(g)) + .changeCase(source == toUpper, start, end); + + if (ap.av.hasHiddenColumns) + { + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + + } + while (end < sg.getEndRes()); + } + ap.seqPanel.seqCanvas.repaint(); } - }); - abovePIDColour.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) + } + else + outputText(evt); + + } + + void outputText(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame); + Vector vseqs = new Vector(); + + String [] selection = ap.av.getViewAsString(true); + SequenceI [] seqs = ap.av.getSelectionAsNewSequence(); + if (selection != null) { - abovePIDColour_itemStateChanged(itemEvent); + for (int i = 0; i < selection.length; i++) + { + Sequence seq = new Sequence( + seqs[i].getName(), + selection[i], + seqs[i].getStart(), seqs[i].getEnd()); + seq.setDescription(seqs[i].getDescription()); + vseqs.addElement( seq ); } - }); + } + + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Selection output - " + e.getActionCommand(), + 600, 500); + + cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( + e.getActionCommand(), + vseqs, + ap.av.showJVSuffix)); + + } + + void addPDB() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + cap.setText("Paste your PDB file here."); + cap.setPDBImport(seq); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300); + } + + private void jbInit() + throws Exception + { + groupMenu.setLabel("Group"); + groupMenu.setLabel("Selection"); + + unGroupMenuItem.setLabel("Remove Group"); + unGroupMenuItem.addActionListener(this); + + nucleotideMenuItem.setLabel("Nucleotide"); + nucleotideMenuItem.addActionListener(this); + conservationMenuItem.addItemListener(this); + abovePIDColour.addItemListener(this); colourMenu.setLabel("Group Colour"); showBoxes.setLabel("Boxes"); showBoxes.setState(true); - showBoxes.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - showBoxes_itemStateChanged(itemEvent); - } - }); + showBoxes.addItemListener(this); showText.setLabel("Text"); - showText.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - showText_itemStateChanged(itemEvent); - } - }); + showText.addItemListener(this); showColourText.setLabel("Colour Text"); - showColourText.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - showColourText_itemStateChanged(itemEvent); - } - }); + showColourText.addItemListener(this); + outputmenu.setLabel("Output to Textbox..."); + seqMenu.setLabel("Sequence"); + pdb.setLabel("View PDB Structure"); + hideSeqs.setLabel("Hide Sequences"); + repGroup.setLabel("Represent Group with"); + revealAll.setLabel("Reveal All"); add(groupMenu); + this.add(seqMenu); + this.add(hideSeqs); + this.add(revealAll); + groupMenu.add(editMenu); + groupMenu.add(outputmenu); + groupMenu.addSeparator(); groupMenu.add(unGroupMenuItem); groupMenu.add(colourMenu); - groupMenu.addSeparator(); groupMenu.add(showBoxes); groupMenu.add(showText); groupMenu.add(showColourText); @@ -204,184 +379,124 @@ public class APopupMenu colourMenu.add(conservationMenuItem); noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); + noColourmenuItem.addActionListener(this); clustalColour.setLabel("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); + clustalColour.addActionListener(this); zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); + zappoColour.addActionListener(this); taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); + taylorColour.addActionListener(this); hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); + hydrophobicityColour.addActionListener(this); helixColour.setLabel("Helix propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(e); - } - }); + helixColour.addActionListener(this); strandColour.setLabel("Strand propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(e); - } - }); + strandColour.addActionListener(this); turnColour.setLabel("Turn propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(e); - } - }); + turnColour.addActionListener(this); buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(e); - } - }); + buriedColour.addActionListener(this); abovePIDColour.setLabel("Above % Identity"); userDefinedColour.setLabel("User Defined"); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); + userDefinedColour.addActionListener(this); PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(e); - } - }); + PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(e); - } - }); + BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel("Conservation"); + editMenu.add(copy); + copy.addActionListener(this); + editMenu.add(cut); + cut.addActionListener(this); + editMenu.add(toUpper); + toUpper.addActionListener(this); + editMenu.add(toLower); + toLower.addActionListener(this); + editMenu.add(toggleCase); + seqMenu.add(pdb); + seqMenu.add(repGroup); + toggleCase.addActionListener(this); + pdb.addActionListener(this); + hideSeqs.addActionListener(this); + repGroup.addActionListener(this); + revealAll.addActionListener(this); + } void refresh() { - SequenceGroup sg = getGroup(); - if(sg!=null) - { - SuperGroup superG = ap.av.alignment.getSuperGroup(sg); - - if (superG != null) - { - superG.setSuperGroupProperties(sg); - } - } ap.seqPanel.seqCanvas.repaint(); + if(ap.overviewPanel!=null) + ap.overviewPanel.updateOverviewImage(); } - protected void clustalColour_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth()); refresh(); } - protected void zappoColour_actionPerformed(ActionEvent e) + protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); } - protected void taylorColour_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); } - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); } - protected void helixColour_actionPerformed(ActionEvent e) + protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); } - protected void strandColour_actionPerformed(ActionEvent e) + protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); } - protected void turnColour_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); } - protected void buriedColour_actionPerformed(ActionEvent e) + protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); } - public void nucleotideMenuItem_actionPerformed(ActionEvent e) + public void nucleotideMenuItem_actionPerformed() { getGroup().cs = new NucleotideColourScheme(); refresh(); } - protected void abovePIDColour_itemStateChanged(ItemEvent ie) + protected void abovePIDColour_itemStateChanged() { SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; + if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, ap.av.alignment.getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); @@ -400,48 +515,50 @@ public class APopupMenu } - protected void userDefinedColour_actionPerformed(ActionEvent e) + protected void userDefinedColour_actionPerformed() { new UserDefinedColours(ap, getGroup()); } - protected void PIDColour_actionPerformed(ActionEvent e) + protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, ap.av.alignment.getWidth())); refresh(); } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void BLOSUM62Colour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, ap.av.alignment.getWidth())); refresh(); } - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); } - protected void conservationMenuItem_itemStateChanged(ItemEvent ie) + protected void conservationMenuItem_itemStateChanged() { SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; if (conservationMenuItem.getState()) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(true), 0, ap.av.alignment.getWidth()); c.calculate(); @@ -460,26 +577,6 @@ public class APopupMenu refresh(); } - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300); - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for (int i = 0; i < sg.sequences.size(); i++) - { - Sequence tmp = (Sequence) sg.sequences.elementAt(i); - sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); - sb.append("\n"); - } - - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); - - } SequenceGroup getGroup() { @@ -492,7 +589,7 @@ public class APopupMenu return sg; } - void unGroupMenuItem_actionPerformed(ActionEvent e) + void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); ap.av.alignment.deleteGroup(sg); @@ -500,22 +597,55 @@ public class APopupMenu ap.repaint(); } - public void showColourText_itemStateChanged(ItemEvent itemEvent) + public void showColourText_itemStateChanged() { getGroup().setColourText(showColourText.getState()); refresh(); } - public void showText_itemStateChanged(ItemEvent itemEvent) + public void showText_itemStateChanged() { getGroup().setDisplayText(showText.getState()); refresh(); } - public void showBoxes_itemStateChanged(ItemEvent itemEvent) + public void showBoxes_itemStateChanged() { getGroup().setDisplayBoxes(showBoxes.getState()); refresh(); } + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if(sg==null || sg.getSize(false)<1) + { + ap.av.hideSequence(new SequenceI[]{seq}); + return; + } + + int gsize = sg.getSize(false); + SequenceI [] hseqs; + + hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ]; + + int index = 0; + for(int i=0; i