X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=d5ddd1bbceb5f055ccc48157be84603ea09a4720;hb=82483c09d45298e6f93a7d3d2b537598cc0451b5;hp=480b1959d49250a5db6c3130ba530e43a1fd7b64;hpb=c5aa740f1fff4c8caee4ccf0c0e0de517ca4dcb8;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 480b195..d5ddd1b 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 @@ -21,11 +21,9 @@ package jalview.gui; import MCview.*; import jalview.analysis.*; - import jalview.datamodel.*; - - import jalview.schemes.*; +import jalview.commands.ChangeCaseCommand; import java.awt.*; import java.awt.event.*; @@ -33,6 +31,7 @@ import java.awt.event.*; import javax.swing.*; import java.util.Vector; +import jalview.io.FormatAdapter; /** @@ -76,6 +75,14 @@ public class PopupMenu extends JPopupMenu 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(); + JMenuItem sequenceFeature = new JMenuItem(); + JMenuItem textColour = new JMenuItem(); + JMenu jMenu1 = new JMenu(); /** * Creates a new PopupMenu object. @@ -109,6 +116,22 @@ 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(); @@ -121,11 +144,14 @@ public class PopupMenu extends JPopupMenu if (seq != null) { + sequenceMenu.setText(sequence.getName()); + JMenuItem menuItem; if( seq.getDatasetSequence().getPDBId() != null) { java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). elements(); + while (e.hasMoreElements()) { final PDBEntry pdb = (PDBEntry) e.nextElement(); @@ -143,7 +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) @@ -151,9 +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()>1) { menuItem = new JMenuItem("Represent Group with " + seq.getName()); menuItem.addActionListener(new java.awt.event.ActionListener() @@ -164,7 +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); + } } @@ -245,14 +306,12 @@ public class PopupMenu extends JPopupMenu { unGroupMenuItem.setVisible(false); } - else - { - groupMenu.insertSeparator(3); - } + if (seq == null) { sequenceMenu.setVisible(false); + pdbMenu.setVisible(false); } if(links != null && links.size()>0) @@ -291,7 +350,10 @@ public class PopupMenu extends JPopupMenu linkMenu.add(item); } - add(linkMenu); + if(sequence!=null) + sequenceMenu.add(linkMenu); + else + add(linkMenu); } } @@ -304,13 +366,13 @@ public class PopupMenu extends JPopupMenu private void jbInit() throws Exception { groupMenu.setText("Group"); - groupMenu.setText("Group"); + groupMenu.setText("Selection"); groupName.setText("Name"); groupName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - groupName_actionPerformed(e); + groupName_actionPerformed(); } }); sequenceMenu.setText("Sequence"); @@ -319,7 +381,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - sequenceName_actionPerformed(e); + sequenceName_actionPerformed(); } }); PIDColour.setFocusPainted(false); @@ -328,7 +390,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - unGroupMenuItem_actionPerformed(e); + unGroupMenuItem_actionPerformed(); } }); @@ -337,7 +399,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - outline_actionPerformed(e); + outline_actionPerformed(); } }); nucleotideMenuItem.setText("Nucleotide"); @@ -345,7 +407,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - nucleotideMenuItem_actionPerformed(e); + nucleotideMenuItem_actionPerformed(); } }); colourMenu.setText("Group Colour"); @@ -355,7 +417,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - showBoxes_actionPerformed(e); + showBoxes_actionPerformed(); } }); showText.setText("Text"); @@ -364,7 +426,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - showText_actionPerformed(e); + showText_actionPerformed(); } }); showColourText.setText("Colour Text"); @@ -372,7 +434,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - showColourText_actionPerformed(e); + showColourText_actionPerformed(); } }); editMenu.setText("Edit"); @@ -381,7 +443,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }); upperCase.setText("To Upper Case"); @@ -389,7 +451,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - upperCase_actionPerformed(e); + changeCase(e); } }); copy.setText("Copy"); @@ -397,7 +459,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }); lowerCase.setText("To Lower Case"); @@ -405,7 +467,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - lowerCase_actionPerformed(e); + changeCase(e); } }); toggle.setText("Toggle Case"); @@ -413,24 +475,63 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - toggle_actionPerformed(e); + changeCase(e); + } + }); + pdbMenu.setText("Associate Structure with Sequence"); + pdbFromFile.setText("From File"); + pdbFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbFromFile_actionPerformed(); + } + }); + enterPDB.setText("Enter PDB Id"); + enterPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + enterPDB_actionPerformed(); + } + }); + discoverPDB.setText("Discover PDB ids"); + discoverPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + discoverPDB_actionPerformed(); + } + }); + outputMenu.setText("Output to Textbox..."); + sequenceFeature.setText("Create Sequence Feature"); + sequenceFeature.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceFeature_actionPerformed(); + } + }); + textColour.setText("Text Colour"); + textColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); } }); + jMenu1.setText("Group"); add(groupMenu); - add(sequenceMenu); - this.add(editMenu); - groupMenu.add(groupName); - groupMenu.addSeparator(); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.addSeparator(); - groupMenu.add(showBoxes); - groupMenu.add(showText); - groupMenu.add(showColourText); - groupMenu.addSeparator(); - groupMenu.add(outline); - sequenceMenu.add(sequenceName); - colourMenu.add(noColourmenuItem); + + add(sequenceMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.add(sequenceFeature); + groupMenu.add(jMenu1); + sequenceMenu.add(sequenceName); + sequenceMenu.add(pdbMenu); + colourMenu.add(textColour); + colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); colourMenu.add(PIDColour); @@ -473,12 +574,22 @@ public class PopupMenu extends JPopupMenu editMenu.add(upperCase); editMenu.add(lowerCase); editMenu.add(toggle); + pdbMenu.add(pdbFromFile); + pdbMenu.add(enterPDB); + pdbMenu.add(discoverPDB); + jMenu1.add(groupName); + jMenu1.add(unGroupMenuItem); + jMenu1.add(colourMenu); + jMenu1.add(showBoxes); + jMenu1.add(showText); + jMenu1.add(showColourText); + jMenu1.add(outline); noColourmenuItem.setText("None"); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(e); + noColourmenuItem_actionPerformed(); } }); @@ -487,7 +598,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - clustalColour_actionPerformed(e); + clustalColour_actionPerformed(); } }); zappoColour.setText("Zappo"); @@ -495,7 +606,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(e); + zappoColour_actionPerformed(); } }); taylorColour.setText("Taylor"); @@ -503,7 +614,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(e); + taylorColour_actionPerformed(); } }); hydrophobicityColour.setText("Hydrophobicity"); @@ -511,7 +622,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - hydrophobicityColour_actionPerformed(e); + hydrophobicityColour_actionPerformed(); } }); helixColour.setText("Helix propensity"); @@ -519,7 +630,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - helixColour_actionPerformed(e); + helixColour_actionPerformed(); } }); strandColour.setText("Strand propensity"); @@ -527,7 +638,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - strandColour_actionPerformed(e); + strandColour_actionPerformed(); } }); turnColour.setText("Turn propensity"); @@ -535,7 +646,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(e); + turnColour_actionPerformed(); } }); buriedColour.setText("Buried Index"); @@ -543,7 +654,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(e); + buriedColour_actionPerformed(); } }); abovePIDColour.setText("Above % Identity"); @@ -551,7 +662,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - abovePIDColour_actionPerformed(e); + abovePIDColour_actionPerformed(); } }); userDefinedColour.setText("User Defined..."); @@ -567,7 +678,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(e); + PIDColour_actionPerformed(); } }); BLOSUM62Colour.setText("BLOSUM62"); @@ -575,7 +686,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(e); + BLOSUM62Colour_actionPerformed(); } }); conservationMenuItem.setText("Conservation"); @@ -583,7 +694,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(e); + conservationMenuItem_actionPerformed(); } }); } @@ -596,7 +707,7 @@ public class PopupMenu extends JPopupMenu if (ap.overviewPanel != null) ap.overviewPanel.updateOverviewImage(); - ap.seqPanel.repaint(); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } /** @@ -604,10 +715,10 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void clustalColour_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, + sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), ap.av.alignment.getWidth()); refresh(); } @@ -617,7 +728,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void zappoColour_actionPerformed(ActionEvent e) + protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); @@ -628,7 +739,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void taylorColour_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); @@ -639,7 +750,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); @@ -650,7 +761,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void helixColour_actionPerformed(ActionEvent e) + protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); @@ -661,7 +772,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void strandColour_actionPerformed(ActionEvent e) + protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); @@ -672,7 +783,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void turnColour_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); @@ -683,7 +794,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void buriedColour_actionPerformed(ActionEvent e) + protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); @@ -694,7 +805,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void nucleotideMenuItem_actionPerformed(ActionEvent e) + public void nucleotideMenuItem_actionPerformed() { getGroup().cs = new NucleotideColourScheme(); refresh(); @@ -705,7 +816,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void abovePIDColour_actionPerformed(ActionEvent e) + protected void abovePIDColour_actionPerformed() { SequenceGroup sg = getGroup(); if(sg.cs==null) @@ -713,8 +824,9 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); @@ -749,18 +861,20 @@ public class PopupMenu extends JPopupMenu sg.cs = udc; } + refresh(); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ - 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, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -769,14 +883,15 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - 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, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -786,7 +901,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); @@ -797,7 +912,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { SequenceGroup sg = getGroup(); if(sg.cs==null) @@ -806,8 +921,10 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, 0, - ap.av.alignment.getWidth()); + ResidueProperties.propHash, 3, + sg.getSequences(ap.av.hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.ConsPercGaps); @@ -830,48 +947,26 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void groupName_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Enter new group name", "Edit group name", - JOptionPane.QUESTION_MESSAGE); - - if (reply == null) - { - return; - } - - sg.setName(reply); - groupName.setText(reply); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void analyze_actionPerformed(ActionEvent e) + protected void groupName_actionPerformed() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); + SequenceGroup sg = getGroup(); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), + " Group Name ", + "Group Description ", + "Edit Group Name/Description"); - for (int i = 0; i < sg.sequences.size(); i++) - { - Sequence tmp = (Sequence) sg.sequences.get(i); - sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); - sb.append("\n"); - } + if (!dialog.accept) + { + return; + } - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); } + /** * DOCUMENT ME! * @@ -892,40 +987,22 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - void sequenceName_actionPerformed(ActionEvent e) + void sequenceName_actionPerformed() { - JLabel idlabel = new JLabel( " Sequence Name "); - JLabel desclabel = new JLabel("Sequence Description "); - idlabel.setFont(new Font("Courier", Font.PLAIN, 12)); - desclabel.setFont(new Font("Courier", Font.PLAIN, 12)); - JTextField id = new JTextField(sequence.getName(), 40); - JTextField description = new JTextField(sequence.getDescription(), 40); - JPanel panel = new JPanel(new BorderLayout()); - JPanel panel2 = new JPanel(new BorderLayout()); - panel2.add(idlabel, BorderLayout.WEST); - panel2.add(id, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.NORTH); - panel2 = new JPanel(new BorderLayout()); - panel2.add(desclabel, BorderLayout.WEST); - panel2.add(description, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.SOUTH); - - - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - panel, "Edit Sequence Name/Description", - JOptionPane.OK_CANCEL_OPTION ); - - - if (reply != JOptionPane.OK_OPTION ) + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), + " Sequence Name ", + "Sequence Description ", + "Edit Sequence Name/Description"); + + if (!dialog.accept) { return; } - String s = id.getText(); - - if (s != null) + if (dialog.getName() != null) { - if (s.indexOf(" ") > -1) + if (dialog.getName().indexOf(" ") > -1) { JOptionPane.showMessageDialog(ap, "Spaces have been converted to \"_\"", @@ -933,14 +1010,15 @@ public class PopupMenu extends JPopupMenu JOptionPane.WARNING_MESSAGE); } - s = s.replace(' ', '_'); - sequence.getDatasetSequence().setName(s); - sequence.setName(s); + sequence.setName(dialog.getName().replace(' ', '_')); ap.repaint(); } - sequence.getDatasetSequence().setDescription(description.getText()); - sequence.setDescription(description.getText()); + sequence.setDescription(dialog.getDescription()); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } /** @@ -948,7 +1026,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - void unGroupMenuItem_actionPerformed(ActionEvent e) + void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); ap.av.alignment.deleteGroup(sg); @@ -962,7 +1040,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void outline_actionPerformed(ActionEvent e) + protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); Color col = JColorChooser.showDialog(this, "Select Outline Colour", @@ -981,7 +1059,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void showBoxes_actionPerformed(ActionEvent e) + public void showBoxes_actionPerformed() { getGroup().setDisplayBoxes(showBoxes.isSelected()); refresh(); @@ -992,7 +1070,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void showText_actionPerformed(ActionEvent e) + public void showText_actionPerformed() { getGroup().setDisplayText(showText.isSelected()); refresh(); @@ -1003,7 +1081,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void showColourText_actionPerformed(ActionEvent e) + public void showColourText_actionPerformed() { getGroup().setColourText(showColourText.isSelected()); refresh(); @@ -1032,77 +1110,240 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); if(sg==null || sg.getSize()<1) { - ap.av.hideSequence(sequence); + ap.av.hideSequence(new SequenceI[]{sequence}); return; } - int index = 0; - while(index < sg.sequences.size()) - { - if(representGroup && sg.getSequenceAt(index)!=sequence) - { - sequence.addHiddenSequence(sg.getSequenceAt(index)); - ap.av.hideSequence(sg.getSequenceAt(index)); - } - else if(!representGroup) - { - ap.av.hideSequence(sg.getSequenceAt(index)); - } - index ++; - } + ap.av.setSelectionGroup(null); - ap.av.setSelectionGroup(null); - refresh(); + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); + + return; + } + + int gsize = sg.getSize(); + SequenceI[] hseqs; + + hseqs = new SequenceI[gsize]; + + int index = 0; + for (int i = 0; i < gsize; i++) + { + hseqs[index++] = sg.getSequenceAt(i); + } + + ap.av.hideSequence(hseqs); } - public void copy_actionPerformed(ActionEvent e) + public void copy_actionPerformed() { ap.alignFrame.copy_actionPerformed(null); } - public void cut_actionPerformed(ActionEvent e) + public void cut_actionPerformed() { ap.alignFrame.cut_actionPerformed(null); } - public void upperCase_actionPerformed(ActionEvent e) + void changeCase(ActionEvent e) { + Object source = e.getSource(); SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null) - return; + Vector regions = new Vector(); + if (sg != null) + { + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do + { + if (ap.av.hasHiddenColumns) + { + 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; + } + + 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==toggle) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if(source==upperCase) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), + startEnd, caseChange + ); + + ap.alignFrame.addHistoryItem(caseCommand); + + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); - for(int g=0; g 0) { - sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1); + PDBEntry entry = new PDBEntry(); + entry.setId(id); + sequence.getDatasetSequence() + .addPDBId(entry); } - ap.repaint(); } - public void toggle_actionPerformed(ActionEvent e) + public void discoverPDB_actionPerformed() + { + new jalview.io.DBRefFetcher( + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); + } + + public void sequenceFeature_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null) + if(sg==null) return; - for (int g = 0; g < sg.getSize(); g++) + int gSize= sg.getSize(); + SequenceI [] seqs = new SequenceI[gSize]; + SequenceFeature [] features = new SequenceFeature[gSize]; + + for (int i = 0; i < gSize; i++) { - sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1); + seqs[i] = sg.getSequenceAt(i).getDatasetSequence(); + int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); + int end = sg.findEndRes(sg.getSequenceAt(i)); + features[i] = new SequenceFeature(null,null, null,start,end,"Jalview"); } - ap.repaint(); + if (ap.seqPanel.seqCanvas.getFeatureRenderer() + .createNewFeatures(seqs, features)) + { + ap.alignFrame.showSeqFeatures.setSelected(true); + ap.av.setShowSequenceFeatures(true); + ap.highlightSearchResults(null); + } } + public void textColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg != null) + new TextColourChooser().chooseColour(ap, sg); + } }