X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e812530c901193acb574caba11c06a5b8fd4142e;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=ca6b199f6b83b44b159d930eb366f107ca56af9f;hpb=f60bd625292b277e70cda0125f04756ac7ca05de;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index ca6b199..e812530 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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 * * This file is part of Jalview. * @@ -70,6 +70,11 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -80,7 +85,7 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; + SequenceI sequence; JMenuItem unGroupMenuItem = new JMenuItem(); @@ -157,7 +162,7 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, + public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links, Vector groupLinks) { // ///////////////////////////////////////////////////////// @@ -183,6 +188,8 @@ public class PopupMenu extends JPopupMenu colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -248,10 +255,67 @@ public class PopupMenu extends JPopupMenu } else { + if (ap.av.alignment.isNucleotide() == false) + { structureMenu.remove(viewStructureMenu); + } // structureMenu.remove(colStructureMenu); } + if (ap.av.alignment.isNucleotide() == true) + { + AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + for (int i = 0; i < aa.length; i++) + { + if (aa[i].getRNAStruc() != null) + { + final String rnastruc = aa[i].getRNAStruc(); + + menuItem = new JMenuItem(); + menuItem.setText("RNA structure - consensus"); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new AppVarna(seq.getSequenceAsString(), rnastruc, seq + .getName(), ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + + // SequenceFeatures[] test = seq.getSequenceFeatures(); + + if (seq.getAnnotation() != null) + { + AlignmentAnnotation seqAnno[] = seq.getAnnotation(); + for (int i = 0; i < seqAnno.length; i++) + { + if (seqAnno[i].getRNAStruc() != null) + { + final String rnastruc = seqAnno[i].getRNAStruc(); + + // TODO: make rnastrucF a bit more nice + menuItem = new JMenuItem(); + menuItem.setText("RNA structure - "+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.getSequenceAsString(), rnastruc, seq + .getName(), ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + } + + + } + menuItem = new JMenuItem("Hide Sequences"); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -371,6 +435,14 @@ public class PopupMenu extends JPopupMenu { clustalColour.setSelected(true); } + else if (sg.cs instanceof PurinePyrimidineColourScheme) + { + purinePyrimidineColour.setSelected(true); + } + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ else { noColourmenuItem.setSelected(true); @@ -391,6 +463,7 @@ public class PopupMenu extends JPopupMenu } // Add a 'show all structures' for the current selection Hashtable pdbe=new Hashtable(); + SequenceI sqass=null; for (SequenceI sq: ap.av.getSequenceSelection()) { Vector pes = (Vector) sq.getDatasetSequence().getPDBId(); @@ -398,6 +471,10 @@ public class PopupMenu extends JPopupMenu for (PDBEntry pe: pes) { pdbe.put(pe.getId(), pe); + if (sqass==null) + { + sqass = sq; + } } } } @@ -405,7 +482,12 @@ public class PopupMenu extends JPopupMenu { final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); final JMenuItem gpdbview; - structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures.")); + 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.")); + } 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() { @@ -435,7 +517,7 @@ public class PopupMenu extends JPopupMenu structureMenu.setVisible(false); } - if (seq !=null && links != null && links.size() > 0) + if (links != null && links.size() > 0) { JMenu linkMenu = new JMenu("Link"); @@ -460,7 +542,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq!=null && urlLink.isDynamic()) { // collect matching db-refs @@ -999,6 +1081,10 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); + if (ap.getAlignment().isNucleotide()) { + colourMenu.add(purinePyrimidineColour); + } + // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1150,6 +1236,21 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); + purinePyrimidineColour.setText("Purine/Pyrimidine"); + purinePyrimidineColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + /* + * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * covariationColour_actionPerformed(); } }); + */ + conservationMenuItem.setText("Conservation"); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -1289,6 +1390,16 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + + /* + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ /** * DOCUMENT ME! * @@ -1772,7 +1883,7 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { - final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[] + final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[] { sequence } : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); Thread discpdb = new Thread(new Runnable()