X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=192899bfb2aa9a349af7075e4f66f40d8cfef0f5;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=613976496d2b226f7e7ec42f32590838b2ff737f;hpb=8f3cf5f09e970ac6e5d9032c03ec29f69fb4b356;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6139764..192899b 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,19 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -24,7 +25,6 @@ import java.awt.event.*; import javax.swing.*; -import MCview.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; @@ -85,6 +85,10 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); + JMenuItem sequenceDetails = new JMenuItem(); + + JMenuItem sequenceSelDetails = new JMenuItem(); + SequenceI sequence; JMenuItem unGroupMenuItem = new JMenuItem(); @@ -162,8 +166,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links, - Vector groupLinks) + public PopupMenu(final AlignmentPanel ap, final SequenceI seq, + Vector links, Vector groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -236,8 +240,10 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence - new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); + // TODO re JAL-860: optionally open dialog or provide a menu entry + // allowing user to open just one structure per sequence + new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] + { pdb })[0], null, ap); // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); } @@ -257,28 +263,29 @@ public class PopupMenu extends JPopupMenu { if (ap.av.getAlignment().isNucleotide() == false) { - structureMenu.remove(viewStructureMenu); + structureMenu.remove(viewStructureMenu); } // structureMenu.remove(colStructureMenu); } if (ap.av.getAlignment().isNucleotide() == true) { - AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { if (aa[i].getRNAStruc() != null) { final String rnastruc = aa[i].getRNAStruc(); - + final String structureLine = aa[i].label; menuItem = new JMenuItem(); - menuItem.setText("RNA structure - consensus"); + menuItem.setText("2D RNA " + structureLine); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - new AppVarna(seq, seq.getSequenceAsString(), rnastruc, seq - .getName(), ap); + new AppVarna(structureLine, seq, seq.getSequenceAsString(), + rnastruc, seq.getName(), ap); } }); viewStructureMenu.add(menuItem); @@ -295,17 +302,18 @@ public class PopupMenu extends JPopupMenu if (seqAnno[i].getRNAStruc() != null) { final String rnastruc = seqAnno[i].getRNAStruc(); - - // TODO: make rnastrucF a bit more nice + + // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); - menuItem.setText("RNA structure - "+seq.getName()); + menuItem.setText("2D RNA - " + seq.getName()); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - new AppVarna(seq,seq.getSequenceAsString(), rnastruc, seq - .getName(), ap); + new AppVarna(seq.getName() + " structure", seq, seq + .getSequenceAsString(), rnastruc, seq.getName(), + ap); } }); viewStructureMenu.add(menuItem); @@ -313,7 +321,6 @@ public class PopupMenu extends JPopupMenu } } - } menuItem = new JMenuItem("Hide Sequences"); @@ -364,7 +371,8 @@ public class PopupMenu extends JPopupMenu } } // for the case when no sequences are even visible - if (ap.av.hasHiddenRows()) { + if (ap.av.hasHiddenRows()) + { { menuItem = new JMenuItem("Reveal All"); menuItem.addActionListener(new ActionListener() @@ -386,9 +394,9 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null&& sg.getSize()>0) + if (sg != null && sg.getSize() > 0) { - groupName.setText("Name: "+sg.getName()); + groupName.setText("Name: " + sg.getName()); groupName.setText("Edit name and description of current group."); if (sg.cs instanceof ZappoColourScheme) @@ -462,36 +470,43 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe=new Hashtable(); - SequenceI sqass=null; - for (SequenceI sq: ap.av.getSequenceSelection()) + Hashtable pdbe = new Hashtable(); + SequenceI sqass = null; + for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = (Vector) sq.getDatasetSequence().getPDBId(); - if (pes!=null) { - for (PDBEntry pe: pes) + Vector pes = (Vector) sq.getDatasetSequence() + .getPDBId(); + if (pes != null) + { + for (PDBEntry pe : pes) { - pdbe.put(pe.getId(), pe); - if (sqass==null) + pdbe.put(pe.getId(), pe); + if (sqass == null) { sqass = sq; } } } } - if (pdbe.size()>0) + if (pdbe.size() > 0) { - final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); + final PDBEntry[] pe = pdbe.values().toArray( + new PDBEntry[pdbe.size()]); final JMenuItem gpdbview; - if (pdbe.size()==1) + if (pdbe.size() == 1) { - structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false))); - } else { - structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures.")); + structureMenu.add(gpdbview = new JMenuItem("View structure for " + + sqass.getDisplayId(false))); + } + else + { + structureMenu.add(gpdbview = new JMenuItem("View all " + + pdbe.size() + " structures.")); } gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment."); gpdbview.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { @@ -542,7 +557,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (seq!=null && urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs @@ -895,6 +910,23 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); + sequenceDetails.setText("Sequence Details ..."); + sequenceDetails.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceDetails_actionPerformed(); + } + }); + sequenceSelDetails.setText("Sequence Details ..."); + sequenceSelDetails + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); PIDColour.setFocusPainted(false); unGroupMenuItem.setText("Remove Group"); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -1052,15 +1084,15 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void * actionPerformed(ActionEvent actionEvent) { * annotationMenuItem_actionPerformed(actionEvent); } }); */ - + groupMenu.add(sequenceSelDetails); add(groupMenu); - add(sequenceMenu); this.add(structureMenu); groupMenu.add(editMenu); @@ -1068,6 +1100,7 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceFeature); groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); + sequenceMenu.add(sequenceDetails); colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -1081,8 +1114,9 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); - if (ap.getAlignment().isNucleotide()) { - colourMenu.add(purinePyrimidineColour); + if (ap.getAlignment().isNucleotide()) + { + colourMenu.add(purinePyrimidineColour); } // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); @@ -1262,6 +1296,44 @@ public class PopupMenu extends JPopupMenu }); } + protected void sequenceSelectionDetails_actionPerformed() + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + + protected void sequenceDetails_actionPerformed() + { + createSequenceDetailsReport(new SequenceI[] + { sequence }); + } + + public void createSequenceDetailsReport(SequenceI[] sequences) + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + StringBuffer contents = new StringBuffer(); + for (SequenceI seq : sequences) + { + contents.append("

Annotation for " + seq.getDisplayId(true) + + "

"); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("

"); + } + cap.setText("" + contents.toString() + ""); + + Desktop.instance.addInternalFrame(cap, "Sequence Details for " + + (sequences.length == 1 ? sequences[0].getDisplayId(true) + : "Selection"), 500, 400); + + } + protected void showNonconserved_actionPerformed() { getGroup().setShowNonconserved(displayNonconserved.isSelected()); @@ -1288,9 +1360,7 @@ public class PopupMenu extends JPopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme( - sg.getSequences(ap.av.getHiddenRepSequences()), - ap.av.getAlignment().getWidth()); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } @@ -1417,8 +1487,8 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1471,8 +1541,8 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1489,8 +1559,8 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1524,8 +1594,8 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -1807,8 +1877,8 @@ public class PopupMenu extends JPopupMenu } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd, - caseChange); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1834,7 +1904,8 @@ public class PopupMenu extends JPopupMenu ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); omitHidden = ap.av.getViewAsString(true); Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] nala = ap.av.getAlignment() + .getAlignmentAnnotation(); if (nala != null) { for (int i = 0; i < nala.length; i++) @@ -1853,8 +1924,10 @@ public class PopupMenu extends JPopupMenu 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 for "+sequence.getDisplayId(false)); - chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'"); + chooser.setDialogTitle("Select a PDB file for " + + sequence.getDisplayId(false)); + chooser.setToolTipText("Load a PDB file and associate it with sequence '" + + sequence.getDisplayId(false) + "'"); int value = chooser.showOpenDialog(null); @@ -1862,7 +1935,8 @@ public class PopupMenu extends JPopupMenu { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true); } } @@ -1948,8 +2022,8 @@ public class PopupMenu extends JPopupMenu public void colourByStructure(String pdbid) { - Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure( - sequence, pdbid); + Annotation[] anots = ap.av.getStructureSelectionManager() + .colourSequenceFromStructure(sequence, pdbid); AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots);