X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=4972874549554961b7a9a79a1c41f93815e1cddb;hb=e3a5770d5844eb5cf183424643605611d3545726;hp=3401cc4b31d676978eb35fa75ec243603051d7ee;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 3401cc4..4972874 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 @@ -59,6 +59,14 @@ public class APopupMenu 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) { @@ -70,6 +78,7 @@ public class APopupMenu ////////////////////////////////////////////////////////// this.ap = apanel; + this.seq = seq; try { @@ -80,6 +89,14 @@ 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(false)>0) @@ -95,8 +112,8 @@ public class APopupMenu } else { + remove(hideSeqs); remove(groupMenu); - remove(editMenu); } if (links!=null) @@ -135,22 +152,21 @@ public class APopupMenu }); linkMenu.add(item); } - add(linkMenu); - if(seq!=null) - { - item = new MenuItem("Show PDB Structure"); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addPDB(seq); - } - }); - - add(item); - } + 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) @@ -180,52 +196,120 @@ 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 || source==toLower || source==toggleCase) - { + {/* SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null) { for (int g = 0; g < sg.getSize(true); g++) { - if (source == toggleCase) - ((SequenceI) sg.getSequences(true).elementAt(g)) - .toggleCase(sg.getStartRes(), sg.getEndRes() + 1); - else - ((SequenceI) sg.getSequences(true).elementAt(g)) - .changeCase(source == toUpper, sg.getStartRes(), - sg.getEndRes() + 1); + 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(); + }*/ + } + 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) + { + 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(Sequence seq) + void addPDB() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); cap.setText("Paste your PDB file here."); @@ -239,7 +323,7 @@ public class APopupMenu throws Exception { groupMenu.setLabel("Group"); - groupMenu.setLabel("Define"); + groupMenu.setLabel("Selection"); unGroupMenuItem.setLabel("Remove Group"); unGroupMenuItem.addActionListener(this); @@ -257,11 +341,22 @@ 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"); 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); @@ -311,7 +406,6 @@ public class APopupMenu BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel("Conservation"); - add(editMenu); editMenu.add(copy); copy.addActionListener(this); editMenu.add(cut); @@ -321,7 +415,13 @@ public class APopupMenu 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); } @@ -514,4 +614,37 @@ 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