X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=206a969d106b2993521607c4f7883fdad9e01701;hb=beca055dbed389362bb692de3c15fa5487c1ebd3;hp=f99b1ed3bc74d4a5d23479734ef3a3fd5bf3ae5e;hpb=fc55c62185b9a614f56e70d860aedbc5e8735fa5;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index f99b1ed..206a969 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 @@ -21,17 +21,20 @@ 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.*; import javax.swing.*; +import java.util.Vector; +import jalview.io.FormatAdapter; +import javax.swing.event.ChangeListener; +import javax.swing.event.ChangeEvent; + /** * DOCUMENT ME! @@ -74,6 +77,14 @@ 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. @@ -81,7 +92,7 @@ public class PopupMenu extends JPopupMenu * @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 @@ -107,6 +118,22 @@ 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(); @@ -119,11 +146,14 @@ 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(); @@ -141,7 +171,7 @@ 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) @@ -149,9 +179,10 @@ 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() @@ -162,7 +193,41 @@ 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); + } } @@ -243,33 +308,38 @@ public class PopupMenu extends JPopupMenu { 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() @@ -282,7 +352,10 @@ public class PopupMenu extends JPopupMenu linkMenu.add(item); } - add(linkMenu); + if(sequence!=null) + sequenceMenu.add(linkMenu); + else + add(linkMenu); } } @@ -295,7 +368,7 @@ 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() { @@ -380,7 +453,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - upperCase_actionPerformed(e); + changeCase(e); } }); copy.setText("Copy"); @@ -396,7 +469,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - lowerCase_actionPerformed(e); + changeCase(e); } }); toggle.setText("Toggle Case"); @@ -404,24 +477,63 @@ 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(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..."); + sequenceFeature.setText("Create Sequence Feature"); + sequenceFeature.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceFeature_actionPerformed(e); + } + }); + textColour.setText("Text Colour"); + textColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(e); + } + }); + 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); @@ -464,6 +576,16 @@ 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() { @@ -587,7 +709,7 @@ public class PopupMenu extends JPopupMenu if (ap.overviewPanel != null) ap.overviewPanel.updateOverviewImage(); - ap.seqPanel.repaint(); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } /** @@ -598,7 +720,7 @@ 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(); } @@ -704,8 +826,9 @@ 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(true), sg.getStartRes(), + sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); @@ -740,6 +863,7 @@ public class PopupMenu extends JPopupMenu sg.cs = udc; } + refresh(); } /** * DOCUMENT ME! @@ -750,8 +874,9 @@ public class PopupMenu extends JPopupMenu { 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(true), + sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -766,8 +891,9 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), + sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -797,8 +923,10 @@ 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(true), + sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.ConsPercGaps); @@ -837,31 +965,6 @@ public class PopupMenu extends JPopupMenu groupName.setText(reply); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void analyze_actionPerformed(ActionEvent e) - { - 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(); - - 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"); - } - - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); - } /** * DOCUMENT ME! @@ -925,13 +1028,15 @@ public class PopupMenu extends JPopupMenu } s = s.replace(' ', '_'); - sequence.getDatasetSequence().setName(s); sequence.setName(s); ap.repaint(); } - sequence.getDatasetSequence().setDescription(description.getText()); sequence.setDescription(description.getText()); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } /** @@ -1021,29 +1126,34 @@ 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()) + for(int i=0; i 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(true), 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(ActionEvent e) + { + new jalview.io.DBRefFetcher( + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); + } + + public void sequenceFeature_actionPerformed(ActionEvent e) { SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null) + if(sg==null) return; - for (int g = 0; g < sg.getSize(); g++) + int gSize= sg.getSize(false); + 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(ActionEvent e) + { + final SequenceGroup sg = getGroup(); + + int original1 = sg.textColour.getRGB(); + int original2 = sg.textColour2.getRGB(); + int thresh = sg.thresholdTextColour; + final JSlider slider = new JSlider(0, 750,sg.thresholdTextColour); + final JButton col1 = new JButton("DARK"); + col1.setBackground(sg.textColour); + col1.setForeground(sg.textColour); + final JButton col2 = new JButton("LIGHT"); + col2.setBackground(sg.textColour2); + col2.setForeground(sg.textColour2); + final JPanel bigpanel = new JPanel(new BorderLayout()); + JPanel panel = new JPanel(); + bigpanel.add(panel, BorderLayout.CENTER); + bigpanel.add(new JLabel( + "Select a dark and light text colour, then set the threshold to" + +"
switch between colours, based on background colour"), + BorderLayout.NORTH); + panel.add(col1); + panel.add(slider); + panel.add(col2); + + col1.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + Color col = JColorChooser.showDialog(bigpanel, + "Select Colour for Text", + sg.textColour); + if (col != null) + { + sg.textColour = col; + col1.setBackground(col); + col1.setForeground(col); + } + ap.repaint(); + } + }); + + col2.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + Color col = JColorChooser.showDialog(bigpanel, + "Select Colour for Text", + sg.textColour); + if (col != null) + { + sg.textColour2 = col; + col2.setBackground(col); + col2.setForeground(col); + } + ap.repaint(); + } + }); + + + slider.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + sg.thresholdTextColour = slider.getValue(); + ap.repaint(); + } + }); + + int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, + bigpanel, + "Adjust Foreground Text Colour Threshold", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE, + null, + null, null); + + if(reply==JOptionPane.CANCEL_OPTION) + { + sg.textColour = new Color(original1); + sg.textColour2 = new Color(original2); + sg.thresholdTextColour = thresh; + } + } }