X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=38385f0f8b58a97ba1285bbd72c6812e11718910;hb=43b415c68805f3dec44a6ddc666d52220483c120;hp=574a2da1a7ba45211d825c3b0032ff166506330d;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java index 574a2da..38385f0 100644 --- a/src/jalview/gui/AppVarnaBinding.java +++ b/src/jalview/gui/AppVarnaBinding.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,8 +20,6 @@ */ package jalview.gui; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -71,6 +69,10 @@ import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.RNA; +import jalview.datamodel.SequenceI; +import jalview.structure.AtomSpec; +import jalview.util.MessageManager; + public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding implements DropTargetListener, InterfaceVARNAListener, MouseListener @@ -103,17 +105,23 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding private JTextField _seq = new JTextField(); - private JLabel _strLabel = new JLabel(MessageManager.getString("label.str")); + private JLabel _strLabel = new JLabel( + MessageManager.getString("label.str")); - private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq")); + private JLabel _seqLabel = new JLabel( + MessageManager.getString("label.seq")); - private JButton _createButton = new JButton(MessageManager.getString("action.create")); + private JButton _createButton = new JButton( + MessageManager.getString("action.create")); - private JButton _updateButton = new JButton(MessageManager.getString("action.update")); + private JButton _updateButton = new JButton( + MessageManager.getString("action.update")); - private JButton _deleteButton = new JButton(MessageManager.getString("action.delete")); + private JButton _deleteButton = new JButton( + MessageManager.getString("action.delete")); - private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot")); + private JButton _duplicateButton = new JButton( + MessageManager.getString("action.snapshot")); protected JPanel _listPanel = new JPanel(); @@ -145,7 +153,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding { // super("VARNA in Jalview"); initVarna(seq, struc); - + } public AppVarnaBinding(ArrayList rnaList) @@ -157,7 +165,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding private void initVarna(String seq, String str) { - + DefaultListModel dlm = new DefaultListModel(); DefaultListSelectionModel m = new DefaultListSelectionModel(); @@ -190,7 +198,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding try { - + vp = new VARNAPanel("0", "."); _RNA1.setRNA(seq, str); _RNA1.drawRNARadiate(vp.getConfig()); @@ -219,7 +227,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding private void initVarnaEdit(ArrayList rnaInList) { - + DefaultListModel dlm = new DefaultListModel(); int marginTools = 40; @@ -243,7 +251,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding FullBackup sel = (FullBackup) _sideList.getSelectedValue(); Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA() .getSize(), sel.rna.getSize()); - //vp.showRNAInterpolated(sel.rna, sel.config, map); + // vp.showRNAInterpolated(sel.rna, sel.config, map); vp.showRNA(sel.rna, sel.config); // _seq.setText(sel.rna.getSeq()); _str.setText(sel.rna.getStructDBN()); @@ -254,12 +262,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding try { - + vp = new VARNAPanel("0", "."); for (int i = 0; i < rnaInList.size(); i++) { rnaInList.get(i).drawRNARadiate(vp.getConfig()); - + } } catch (ExceptionNonEqualLength e) { @@ -346,7 +354,9 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding ops.add(_deleteButton); ops.add(_duplicateButton); - JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER); + JLabel j = new JLabel( + MessageManager.getString("label.structures_manager"), + JLabel.CENTER); _listPanel.setLayout(new BorderLayout()); // _listPanel.add(ops, BorderLayout.SOUTH); @@ -809,17 +819,16 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding public void onUINewStructure(VARNAConfig v, RNA r) { // patch to fix infinite loop - // The problem is that onUINewStructure is called when user clicks + // The problem is that onUINewStructure is called when user clicks // check with Yann about whether Jalview should do anything with this event. - // e.g. if user has used VARNA's menu to import a structure .. Jalview may need to be told which structure is displayed. - + // e.g. if user has used VARNA's menu to import a structure .. Jalview may + // need to be told which structure is displayed. + // _rnaList.add(v, r, "", true); } public void onWarningEmitted(String s) { - // TODO Auto-generated method stub - } public void mouseClicked(MouseEvent e) @@ -843,127 +852,79 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding public void mouseEntered(MouseEvent arg0) { - // TODO Auto-generated method stub - } public void mouseExited(MouseEvent arg0) { - // TODO Auto-generated method stub - } public void mousePressed(MouseEvent arg0) { - // TODO Auto-generated method stub - } public void mouseReleased(MouseEvent arg0) { - // TODO Auto-generated method stub - - } - - @Override - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbId) - { - // TODO Auto-generated method stub - return null; } @Override public String[] getPdbFile() { - // TODO Auto-generated method stub return null; } @Override - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbId) - { - // TODO Auto-generated method stub - - } - - @Override - public void mouseOverStructure(int atomIndex, String strInfo) - { - // TODO Auto-generated method stub - - } - - @Override public void releaseReferences(Object svl) { - // TODO Auto-generated method stub - } @Override public void updateColours(Object source) { - // TODO Auto-generated method stub - } @Override public void componentHidden(ComponentEvent e) { - // TODO Auto-generated method stub - } @Override public void componentMoved(ComponentEvent e) { - // TODO Auto-generated method stub - } @Override public void componentResized(ComponentEvent e) { - // TODO Auto-generated method stub - } @Override public void componentShown(ComponentEvent e) { - // TODO Auto-generated method stub - } @Override public void onStructureRedrawn() { - // TODO Auto-generated method stub - } @Override public void onZoomLevelChanged() { - // TODO Auto-generated method stub - } @Override public void onTranslationChanged() { - // TODO Auto-generated method stub - } -} -/* - * public static void main(String[] args) { JTextField str = new - * JTextField("ATGC"); - * - * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str); - * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - * vab.varnagui.pack(); vab.varnagui.setVisible(true); } } - */ + @Override + public void highlightAtoms(List atoms) + { + } + + @Override + public boolean isListeningFor(SequenceI seq) + { + return true; + } +}