X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=f786bde5dfaba8b787b6363c7f4c7b6539b81bbd;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=6393f749a9cd6f00126ca0462bb13524f268ff56;hpb=568011c82e003d19f533147e6429407ca56b67ec;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 6393f74..f786bde 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 @@ -26,6 +26,7 @@ import java.util.Vector; import jalview.analysis.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.commands.ChangeCaseCommand; public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener @@ -58,6 +59,16 @@ public class APopupMenu 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(); + Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { @@ -69,6 +80,7 @@ public class APopupMenu ////////////////////////////////////////////////////////// this.ap = apanel; + this.seq = seq; try { @@ -79,25 +91,34 @@ 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 && sg.getSize()>0) + 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); + } + } else { + remove(hideSeqs); remove(groupMenu); } - if (!ap.av.alignment.getGroups().contains(sg)) - { - groupMenu.remove(unGroupMenuItem); - } - - if (seq != null && links!=null) + if (links!=null) { Menu linkMenu = new Menu("Link"); MenuItem item; @@ -107,13 +128,22 @@ public class APopupMenu link = links.elementAt(i).toString(); final String target = link.substring(0, link.indexOf("|")); item = new MenuItem(target); - String id = seq.getName(); - if(id.indexOf("|")>-1) - id = id.substring(id.lastIndexOf("|")+1); - final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$")) - + id + - 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); item.addActionListener(new java.awt.event.ActionListener() { @@ -124,21 +154,21 @@ public class APopupMenu }); linkMenu.add(item); } - add(linkMenu); - - item = new MenuItem("Show PDB Structure"); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addPDB(seq); - } - }); - - add(item); - - + 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); } public void itemStateChanged(ItemEvent evt) @@ -168,60 +198,152 @@ public class APopupMenu helixColour_actionPerformed(); else if(source==strandColour) strandColour_actionPerformed(); - else if(source==clustalColour) + 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) + else if (source == userDefinedColour) + userDefinedColour_actionPerformed(); + else if (source == PIDColour) + PIDColour_actionPerformed(); + else if (source == BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); - else if(source==noColourmenuItem) + else if (source == noColourmenuItem) noColourmenuItem_actionPerformed(); - else if(source==conservationMenuItem) - conservationMenuItem_itemStateChanged(); - else if(source==unGroupMenuItem) + 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) + { + ap.av.showAllHiddenSeqs(); + } + else if(source==copy) ap.alignFrame.copy_actionPerformed(); else if(source==cut) ap.alignFrame.cut_actionPerformed(); - else if(source==toUpper) + else if(source==toUpper || source==toLower || source==toggleCase) { - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + SequenceGroup sg = ap.av.getSelectionGroup(); + Vector regions = new Vector(); + if (sg != null) + { + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do { - for (int g = 0; g < sg.getSize(); g++) + if (ap.av.hasHiddenColumns) { - sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), - sg.getEndRes() + 1); + if(start==0) + start = ap.av.colSel.adjustForHiddenColumns(start); + + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + end = sg.getEndRes() + 1; + if (end > sg.getEndRes()) + end = sg.getEndRes() + 1; } - ap.seqPanel.seqCanvas.repaint(); + + regions.addElement(new int[] + {start, end}); + + if (ap.av.hasHiddenColumns) + { + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + } + while (end < sg.getEndRes()); + + int[][] startEnd = new int[regions.size()][2]; + for (int i = 0; i < regions.size(); i++) + { + startEnd[i] = (int[]) regions.elementAt(i); + } + + + String description; + int caseChange; + + if(source==toggleCase) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if(source==toUpper) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(true), startEnd, caseChange + ); + + ap.alignFrame.addHistoryItem(caseCommand); + + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } - else if(source==toLower) - { - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + } + else + outputText(evt); + + } + + void outputText(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + Vector vseqs = new Vector(); + + String [] selection = ap.av.getViewAsString(true); + SequenceI [] seqs = ap.av.getSelectionAsNewSequence(); + if (selection != null) { - for (int g = 0; g < sg.getSize(); g++) + for (int i = 0; i < selection.length; i++) { - sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), - sg.getEndRes() + 1); - } - ap.seqPanel.seqCanvas.repaint(); + 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(Sequence seq) + void addPDB() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); cap.setText("Paste your PDB file here."); @@ -235,7 +357,7 @@ public class APopupMenu throws Exception { groupMenu.setLabel("Group"); - groupMenu.setLabel("Define"); + groupMenu.setLabel("Selection"); unGroupMenuItem.setLabel("Remove Group"); unGroupMenuItem.addActionListener(this); @@ -253,14 +375,20 @@ public class APopupMenu showText.addItemListener(this); showColourText.setLabel("Colour Text"); 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"); + menu1.setLabel("Group"); add(groupMenu); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.addSeparator(); - groupMenu.add(showBoxes); - groupMenu.add(showText); - groupMenu.add(showColourText); + this.add(seqMenu); + this.add(hideSeqs); + this.add(revealAll); + groupMenu.add(editMenu); + groupMenu.add(outputmenu); + groupMenu.add(menu1); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); @@ -307,7 +435,6 @@ public class APopupMenu BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel("Conservation"); - add(editMenu); editMenu.add(copy); copy.addActionListener(this); editMenu.add(cut); @@ -316,6 +443,19 @@ public class APopupMenu toUpper.addActionListener(this); editMenu.add(toLower); toLower.addActionListener(this); + editMenu.add(toggleCase); + seqMenu.add(pdb); + seqMenu.add(repGroup); + menu1.add(unGroupMenuItem); + menu1.add(colourMenu); + menu1.add(showBoxes); + menu1.add(showText); + menu1.add(showColourText); + toggleCase.addActionListener(this); + pdb.addActionListener(this); + hideSeqs.addActionListener(this); + repGroup.addActionListener(this); + revealAll.addActionListener(this); } @@ -329,7 +469,7 @@ public class APopupMenu 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(); } @@ -389,7 +529,7 @@ public class APopupMenu 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()); @@ -417,7 +557,7 @@ public class APopupMenu { 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(); } @@ -428,7 +568,7 @@ public class APopupMenu 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(); @@ -451,7 +591,7 @@ public class APopupMenu Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(true), 0, ap.av.alignment.getWidth()); c.calculate(); @@ -508,4 +648,37 @@ public class APopupMenu 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