X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=356e5d57b9bd68605c02c99452e8e1fd28ea9930;hb=c3c305755d392741176209a0274a47897ac4d8a8;hp=4f2326a1b955a1f65b3cc60377b3a6b395d7a28c;hpb=aa397119f56e13b217d0a55d19dd1026118eddce;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 4f2326a..356e5d5 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.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 @@ -32,6 +32,9 @@ import java.awt.event.*; import javax.swing.*; +import java.util.Vector; +import jalview.io.FormatAdapter; + /** * DOCUMENT ME! @@ -68,14 +71,25 @@ public class PopupMenu extends JPopupMenu JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); - - /** + JMenu editMenu = new JMenu(); + JMenuItem cut = new JMenuItem(); + JMenuItem copy = new JMenuItem(); + JMenuItem upperCase = new JMenuItem(); + JMenuItem lowerCase = new JMenuItem(); + JMenuItem toggle = new JMenuItem(); + JMenu pdbMenu = new JMenu(); + JMenuItem pdbFromFile = new JMenuItem(); + JMenuItem enterPDB = new JMenuItem(); + JMenuItem discoverPDB = new JMenuItem(); + JMenu outputMenu = new JMenu(); + + /** * Creates a new PopupMenu object. * * @param ap DOCUMENT ME! * @param seq DOCUMENT ME! */ - public PopupMenu(final AlignmentPanel ap, Sequence seq) + public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) { /////////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -101,6 +115,22 @@ public class PopupMenu extends JPopupMenu colours.add(PIDColour); colours.add(BLOSUM62Colour); + for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) + { + JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] ); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputMenu.add(item); + } + + try { jbInit(); @@ -113,11 +143,15 @@ public class PopupMenu extends JPopupMenu if (seq != null) { + int start = Math.max(sequence.getName().length()-15, 0); + sequenceMenu.setText(sequence.getName().substring(start)); + JMenuItem menuItem; if( seq.getDatasetSequence().getPDBId() != null) { java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). elements(); + while (e.hasMoreElements()) { final PDBEntry pdb = (PDBEntry) e.nextElement(); @@ -135,7 +169,7 @@ public class PopupMenu extends JPopupMenu } } - /* menuItem = new JMenuItem("Hide Sequences"); + menuItem = new JMenuItem("Hide Sequences"); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -143,9 +177,10 @@ public class PopupMenu extends JPopupMenu hideSequences(false); } }); - sequenceMenu.add(menuItem); + add(menuItem); - if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1) + if(ap.av.getSelectionGroup() !=null + && ap.av.getSelectionGroup().getSize(false)>1) { menuItem = new JMenuItem("Represent Group with " + seq.getName()); menuItem.addActionListener(new java.awt.event.ActionListener() @@ -156,7 +191,41 @@ public class PopupMenu extends JPopupMenu } }); sequenceMenu.add(menuItem); - }*/ + } + + if (ap.av.hasHiddenRows) + { + final int index = ap.av.alignment.findIndex(seq); + + if (ap.av.adjustForHiddenSeqs(index) - + ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + menuItem = new JMenuItem("Reveal Sequences"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showSequence(index); + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); + } + }); + add(menuItem); + } + + menuItem = new JMenuItem("Reveal All"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showAllHiddenSeqs(); + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); + } + }); + + add(menuItem); + } } @@ -227,38 +296,48 @@ public class PopupMenu extends JPopupMenu showColourText.setSelected(sg.getColourText()); showBoxes.setSelected(sg.getDisplayBoxes()); } + else + { + groupMenu.setVisible(false); + editMenu.setVisible(false); + } if (!ap.av.alignment.getGroups().contains(sg)) { unGroupMenuItem.setVisible(false); } - else - { - groupMenu.insertSeparator(3); - } + if (seq == null) { sequenceMenu.setVisible(false); + pdbMenu.setVisible(false); } - else - { - java.util.Vector links = Preferences.sequenceURLLinks; + if(links != null && links.size()>0) + { JMenu linkMenu = new JMenu("Link"); JMenuItem item; for(int i=0; i-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); + 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() @@ -271,7 +350,10 @@ public class PopupMenu extends JPopupMenu linkMenu.add(item); } - add(linkMenu); + if(sequence!=null) + sequenceMenu.add(linkMenu); + else + add(linkMenu); } } @@ -284,7 +366,7 @@ public class PopupMenu extends JPopupMenu private void jbInit() throws Exception { groupMenu.setText("Group"); - groupMenu.setText("Define"); + groupMenu.setText("Selection"); groupName.setText("Name"); groupName.addActionListener(new java.awt.event.ActionListener() { @@ -355,20 +437,89 @@ public class PopupMenu extends JPopupMenu showColourText_actionPerformed(e); } }); - add(groupMenu); - add(sequenceMenu); - groupMenu.add(groupName); - groupMenu.addSeparator(); - groupMenu.add(unGroupMenuItem); + editMenu.setText("Edit"); + cut.setText("Cut"); + cut.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(e); + } + }); + upperCase.setText("To Upper Case"); + upperCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + upperCase_actionPerformed(e); + } + }); + copy.setText("Copy"); + copy.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(e); + } + }); + lowerCase.setText("To Lower Case"); + lowerCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + lowerCase_actionPerformed(e); + } + }); + toggle.setText("Toggle Case"); + toggle.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + toggle_actionPerformed(e); + } + }); + pdbMenu.setText("Associate Structure with Sequence"); + pdbFromFile.setText("From File"); + pdbFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbFromFile_actionPerformed(e); + } + }); + enterPDB.setText("Enter PDB Id"); + enterPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + enterPDB_actionPerformed(e); + } + }); + discoverPDB.setText("Discover PDB ids"); + discoverPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + discoverPDB_actionPerformed(e); + } + }); + outputMenu.setText("Output to Textbox..."); + add(groupMenu); + + add(sequenceMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.addSeparator(); + groupMenu.add(groupName); + groupMenu.add(unGroupMenuItem); groupMenu.add(colourMenu); - groupMenu.addSeparator(); - groupMenu.add(showBoxes); + groupMenu.add(showBoxes); groupMenu.add(showText); groupMenu.add(showColourText); - groupMenu.addSeparator(); - groupMenu.add(outline); + groupMenu.add(outline); sequenceMenu.add(sequenceName); - colourMenu.add(noColourmenuItem); + sequenceMenu.add(pdbMenu); + colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); colourMenu.add(PIDColour); @@ -406,7 +557,15 @@ public class PopupMenu extends JPopupMenu colourMenu.addSeparator(); colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); - noColourmenuItem.setText("None"); + editMenu.add(copy); + editMenu.add(cut); + editMenu.add(upperCase); + editMenu.add(lowerCase); + editMenu.add(toggle); + pdbMenu.add(pdbFromFile); + pdbMenu.add(enterPDB); + pdbMenu.add(discoverPDB); + noColourmenuItem.setText("None"); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -529,7 +688,7 @@ public class PopupMenu extends JPopupMenu if (ap.overviewPanel != null) ap.overviewPanel.updateOverviewImage(); - ap.seqPanel.repaint(); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } /** @@ -540,7 +699,7 @@ public class PopupMenu extends JPopupMenu protected void clustalColour_actionPerformed(ActionEvent e) { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, + sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth()); refresh(); } @@ -646,7 +805,8 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { - 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, @@ -692,7 +852,7 @@ public class PopupMenu extends JPopupMenu { 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(); } @@ -708,7 +868,7 @@ public class PopupMenu extends JPopupMenu 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(); @@ -739,7 +899,8 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, 0, + ResidueProperties.propHash, 3, + sg.getSequences(true), 0, ap.av.alignment.getWidth()); c.calculate(); @@ -794,9 +955,9 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); StringBuffer sb = new StringBuffer(); - for (int i = 0; i < sg.sequences.size(); i++) + for (int i = 0; i < sg.getSize(false); i++) { - Sequence tmp = (Sequence) sg.sequences.get(i); + Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i); sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); sb.append("\n"); } @@ -963,29 +1124,190 @@ public class PopupMenu extends JPopupMenu void hideSequences(boolean representGroup) { SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null || sg.getSize()<1) + if(sg==null || sg.getSize(false)<1) { - ap.av.hideSequence(sequence); + ap.av.hideSequence(new SequenceI[]{sequence}); return; } + int gsize = sg.getSize(false); + SequenceI [] hseqs; + + hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ]; + int index = 0; - while(index < sg.sequences.size()) + while(index < gsize) { if(representGroup && sg.getSequenceAt(index)!=sequence) { sequence.addHiddenSequence(sg.getSequenceAt(index)); - ap.av.hideSequence(sg.getSequenceAt(index)); + hseqs[index] = sg.getSequenceAt(index); } else if(!representGroup) { - ap.av.hideSequence(sg.getSequenceAt(index)); + hseqs[index] = sg.getSequenceAt(index); } index ++; } + ap.av.hideSequence(hseqs); + ap.av.setSelectionGroup(null); - refresh(); } + public void copy_actionPerformed(ActionEvent e) + { + ap.alignFrame.copy_actionPerformed(null); + } + + public void cut_actionPerformed(ActionEvent e) + { + ap.alignFrame.cut_actionPerformed(null); + } + + public void upperCase_actionPerformed(ActionEvent e) + { + changeCase(e.getSource()); + } + + public void lowerCase_actionPerformed(ActionEvent e) + { + changeCase(e.getSource()); + } + + public void toggle_actionPerformed(ActionEvent e) + { + changeCase(e.getSource()); + } + + void changeCase(Object source) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) + { + 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 == toggle) + ( (SequenceI) sg.getSequences(true).elementAt(g)) + .toggleCase(start, end); + else + ( (SequenceI) sg.getSequences(true).elementAt(g)) + .changeCase(source == upperCase, start, end); + + if (ap.av.hasHiddenColumns) + { + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + + } + while (end < sg.getEndRes()); + } + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + } + } + + public void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, + 500); + + String [] omitHidden = null; + + if(ap.av.hasHiddenColumns) + { + System.out.println("PROMPT USER HERE"); + omitHidden = ap.av.getViewAsString(true); + } + + cap.setText(new FormatAdapter().formatSequences( + e.getActionCommand(), + ap.av.getSelectionAsNewSequence(), + omitHidden)); + } + + + public void pdbFromFile_actionPerformed(ActionEvent e) + { + jalview.io.JalviewFileChooser chooser + = new jalview.io.JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY")); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Select a PDB file"); + chooser.setToolTipText("Load a PDB file"); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + PDBEntry entry = new PDBEntry(); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + try + { + MCview.PDBfile pdbfile = new MCview.PDBfile(choice, + jalview.io.AppletFormatAdapter.FILE); + + if (pdbfile.id == null) + { + String reply = JOptionPane.showInternalInputDialog( + Desktop.desktop, + "Couldn't find a PDB id in the file supplied." + + "Please enter an Id to identify this structure.", + "No PDB Id in File", JOptionPane.QUESTION_MESSAGE); + if (reply == null) + return; + + entry.setId(reply); + } + else + entry.setId(pdbfile.id); + } + catch (java.io.IOException ex) + { + ex.printStackTrace(); + } + + entry.setFile(choice); + sequence.getDatasetSequence().addPDBId(entry); + } + + } + + public void enterPDB_actionPerformed(ActionEvent e) + { + String id = JOptionPane.showInternalInputDialog(Desktop.desktop, + "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE); + + if (id != null && id.length() > 0) + { + PDBEntry entry = new PDBEntry(); + entry.setId(id); + sequence.getDatasetSequence() + .addPDBId(entry); + } + } + + public void discoverPDB_actionPerformed(ActionEvent e) + { + new jalview.io.DBRefFetcher( + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); + } }