X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=23d04b7ab82b5f6637282d817e667d492bd3735d;hb=2ef43e1e505af2742f1c3a59619c8a4357ea82c4;hp=34ffd4c9f29b404fd1ae937dfe0dfcb5d7133cfb;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 34ffd4c..23d04b7 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -33,6 +33,7 @@ import java.awt.event.*; import javax.swing.*; import java.util.Vector; +import jalview.io.FormatAdapter; /** @@ -76,6 +77,11 @@ 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(); /** * Creates a new PopupMenu object. @@ -109,6 +115,23 @@ public class PopupMenu extends JPopupMenu colours.add(PIDColour); colours.add(BLOSUM62Colour); + for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++) + { + JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats. + elementAt( + i)); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputMenu.add(item); + } + + try { jbInit(); @@ -121,11 +144,15 @@ 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(); @@ -151,7 +178,7 @@ public class PopupMenu extends JPopupMenu hideSequences(false); } }); - sequenceMenu.add(menuItem); + add(menuItem); if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize(false)>1) @@ -174,7 +201,7 @@ public class PopupMenu extends JPopupMenu if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) { - menuItem = new JMenuItem("Reveal"); + menuItem = new JMenuItem("Reveal Sequences"); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -185,7 +212,7 @@ public class PopupMenu extends JPopupMenu ap.overviewPanel.updateOverviewImage(); } }); - sequenceMenu.add(menuItem); + add(menuItem); } menuItem = new JMenuItem("Reveal All"); @@ -200,10 +227,7 @@ public class PopupMenu extends JPopupMenu } }); - sequenceMenu.add(menuItem); - - - + add(menuItem); } @@ -285,14 +309,12 @@ 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) @@ -331,7 +353,10 @@ public class PopupMenu extends JPopupMenu linkMenu.add(item); } - add(linkMenu); + if(sequence!=null) + sequenceMenu.add(linkMenu); + else + add(linkMenu); } } @@ -344,7 +369,7 @@ 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() { @@ -456,21 +481,48 @@ public class PopupMenu extends JPopupMenu 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); - this.add(editMenu); + + add(sequenceMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.addSeparator(); groupMenu.add(groupName); - groupMenu.addSeparator(); - groupMenu.add(unGroupMenuItem); + 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); @@ -513,6 +565,9 @@ public class PopupMenu extends JPopupMenu 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() { @@ -1094,6 +1149,7 @@ public class PopupMenu extends JPopupMenu } ap.av.setSelectionGroup(null); + ap.repaint(); refresh(); } @@ -1150,4 +1206,105 @@ public class PopupMenu extends JPopupMenu ap.repaint(); } + 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) + { + int size = (ap.av.getSelectionGroup() == null ? 0 : + ap.av.getSelectionGroup().getSize(false)); + + if (size == 0 || size > 1) + { + JOptionPane.showInternalMessageDialog( + Desktop.desktop, + "Select a single sequence to specify a PDB id for first", + "Select Single Selected", JOptionPane.WARNING_MESSAGE); + return; + } + + 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); + ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence() + .addPDBId(entry); + } + } + + public void discoverPDB_actionPerformed(ActionEvent e) + { + new jalview.io.DBRefFetcher( + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); + } }