label.export_image = Export Image
label.vamsas_store = VAMSAS store
label.translate_cDNA = Translate as cDNA
-label.linked_view_title = Linked cDNA and protein view
+label.reverse = Reverse
+label.reverse_complement = Reverse Complement
+label.linked_view_title = Linked CDS and protein view
label.align = Align
label.extract_scores = Extract Scores
label.get_cross_refs = Get Cross-References
label.eps_file = EPS file
label.png_image = PNG image
status.saving_file = Saving {0}
- status.export_complete = Export complete.
+ status.export_complete = {0} Export completed.
status.fetching_pdb = Fetching PDB {0}
status.refreshing_news = Refreshing news
status.importing_vamsas_session_from = Importing VAMSAS session from {0}
label.nw_mapping = Needleman & Wunsch Alignment
label.sifts_mapping = SIFTs Mapping
label.mapping_method = Sequence \u27f7 Structure mapping method
++label.mapping_method = Sequence \u27f7 Structure mapping method
+ status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file.
+ status.cancelled_image_export_operation = Cancelled {0} export operation.
+ info.error_creating_file = Error creating {0} file.
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
-import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
public void setGUINucleotide(boolean nucleotide)
{
showTranslation.setVisible(nucleotide);
+ showReverse.setVisible(nucleotide);
+ showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
return;
}
- format = new IdentifyFile().Identify(str, "Paste");
+ format = new IdentifyFile().identify(str, "Paste");
} catch (OutOfMemoryError er)
{
// TODO 1: no mappings are set up for EMBL product
// TODO 2: if they were, should add them to protein alignment, not
// dna
- Set<AlignedCodonFrame> cf = prods.getCodonFrames();
+ List<AlignedCodonFrame> cf = prods.getCodonFrames();
for (AlignedCodonFrame acf : cf)
{
al.addCodonFrame(acf);
}
- AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
+ AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
- String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
- + " for " + ((isRegSel) ? "selected region of " : "")
+ String newtitle = "" + (dna ? "Proteins" : "Nucleotides")
+ + " for " + (isRegSel ? "selected region of " : "")
+ getTitle();
- naf.setTitle(newtitle);
+ newFrame.setTitle(newtitle);
- // temporary flag until SplitFrame is released
boolean asSplitFrame = Cache.getDefault(
Preferences.ENABLE_SPLIT_FRAME, true);
if (asSplitFrame)
.getSequenceSelection();
if (dna)
{
- copyAlignment = AlignmentUtils.makeExonAlignment(
+ copyAlignment = AlignmentUtils.makeCdsAlignment(
sequenceSelection, cf);
al.getCodonFrames().clear();
al.getCodonFrames().addAll(cf);
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
copyThis.setTitle(AlignFrame.this.getTitle());
// SplitFrame with dna above, protein below
- SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
- dna ? naf : copyThis);
- naf.setVisible(true);
+ boolean showSequenceFeatures = viewport
+ .isShowSequenceFeatures();
+ newFrame.setShowSeqFeatures(showSequenceFeatures);
+ copyThis.setShowSeqFeatures(showSequenceFeatures);
+ FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ /*
+ * copy feature rendering settings to split frame
+ */
+ newFrame.alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer().transferSettings(
+ myFeatureStyling);
+ copyThis.alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer().transferSettings(
+ myFeatureStyling);
+ SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
+ dna ? newFrame : copyThis);
+ newFrame.setVisible(true);
copyThis.setVisible(true);
String linkedTitle = MessageManager
.getString("label.linked_view_title");
}
else
{
- Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
}
}
String type = null;
try
{
- type = new IdentifyFile().Identify(file, protocol);
+ type = new IdentifyFile().identify(file, protocol);
} catch (Exception ex)
{
type = null;
/**
* Attempt to load a "dropped" file or URL string: First by testing whether
- * it's and Annotation file, then a JNet file, and finally a features file. If
+ * it's an Annotation file, then a JNet file, and finally a features file. If
* all are false then the user may have dropped an alignment file onto this
* AlignFrame.
*
{
if (protocol == null)
{
- protocol = jalview.io.FormatAdapter.checkProtocol(file);
+ protocol = FormatAdapter.checkProtocol(file);
}
// if the file isn't identified, or not positively identified as some
// other filetype (PFAM is default unidentified alignment file type) then
// try to parse it as a features file
if (format == null)
{
- format = new IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
if (format.equalsIgnoreCase("JnetFile"))
{
viewport.setColumnSelection(cs);
isAnnotation = true;
}
- else
+ else if (IdentifyFile.FeaturesFile.equals(format))
{
- /*
- * if (format.equalsIgnoreCase("PDB")) {
- *
- * String pdbfn = ""; // try to match up filename with sequence id
- * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
- * new File(file); pdbfn = fl.getName(); } else if (protocol ==
- * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
- * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
- * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
- * // attempt to find a match in the alignment SequenceI mtch =
- * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
- * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
- * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
- * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
- * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
- * { System.err.println("Associated file : " + file + " with " +
- * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
- * TODO: maybe need to load as normal otherwise return; } }
- */
- // try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
+ if (parseFeaturesFile(file, protocol))
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ alignPanel.paintAlignment(true);
}
+ }
else
{
- alignPanel.paintAlignment(true);
+ new FileLoader().LoadFile(viewport, file, protocol, format);
}
- }
}
}
if (isAnnotation)
} catch (Exception x)
{
}
- ;
new OOMWarning(
"loading data "
+ (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
{
// TODO no longer a menu action - refactor as required
final AlignmentI alignment = getViewport().getAlignment();
- Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
if (mappings == null)
{
return;
sf.setComplementVisible(this, show);
}
}
+
+ /**
+ * Generate the reverse (optionally complemented) of the selected sequences,
+ * and add them to the alignment
+ */
+ @Override
+ protected void showReverse_actionPerformed(boolean complement)
+ {
+ AlignmentI al = null;
+ try
+ {
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+ al = dna.reverseCdna(complement);
+ viewport.addAlignment(al, "");
+ } catch (Exception ex)
+ {
+ System.err.println(ex.getMessage());
+ return;
+ }
+ }
}
class PrintThread extends Thread
this.delegate = delegate;
}
+ @Override
public void activateFrame(JInternalFrame f)
{
try
}
}
+ @Override
public void beginDraggingFrame(JComponent f)
{
delegate.beginDraggingFrame(f);
}
+ @Override
public void beginResizingFrame(JComponent f, int direction)
{
delegate.beginResizingFrame(f, direction);
}
+ @Override
public void closeFrame(JInternalFrame f)
{
delegate.closeFrame(f);
}
+ @Override
public void deactivateFrame(JInternalFrame f)
{
delegate.deactivateFrame(f);
}
+ @Override
public void deiconifyFrame(JInternalFrame f)
{
delegate.deiconifyFrame(f);
}
+ @Override
public void dragFrame(JComponent f, int newX, int newY)
{
if (newY < 0)
delegate.dragFrame(f, newX, newY);
}
+ @Override
public void endDraggingFrame(JComponent f)
{
delegate.endDraggingFrame(f);
}
+ @Override
public void endResizingFrame(JComponent f)
{
delegate.endResizingFrame(f);
}
+ @Override
public void iconifyFrame(JInternalFrame f)
{
delegate.iconifyFrame(f);
}
+ @Override
public void maximizeFrame(JInternalFrame f)
{
delegate.maximizeFrame(f);
}
+ @Override
public void minimizeFrame(JInternalFrame f)
{
delegate.minimizeFrame(f);
}
+ @Override
public void openFrame(JInternalFrame f)
{
delegate.openFrame(f);
delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
}
+ @Override
public void setBoundsForFrame(JComponent f, int newX, int newY,
int newWidth, int newHeight)
{
this.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
quit();
MouseAdapter ma;
this.addMouseListener(ma = new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (SwingUtilities.isRightMouseButton(evt))
// Spawn a thread that shows the splashscreen
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
new SplashScreen();
// takes to open it later on.
new Thread(new Runnable()
{
+ @Override
public void run()
{
Cache.log.debug("Filechooser init thread started.");
// reselected again.
boolean refresh = true;
+ @Override
public void menuCanceled(MenuEvent e)
{
refresh = true;
}
+ @Override
public void menuDeselected(MenuEvent e)
{
refresh = true;
}
+ @Override
public void menuSelected(MenuEvent e)
{
if (refresh)
MessageManager.getString("label.paste_new_window"));
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
paste();
String file = (String) contents
.getTransferData(DataFlavor.stringFlavor);
- String format = new IdentifyFile().Identify(file,
+ String format = new IdentifyFile().identify(file,
FormatAdapter.PASTE);
new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
final JMenuItem menuItem = new JMenuItem(title);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameActivated(
javax.swing.event.InternalFrameEvent evt)
{
}
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
try
}
}
+ @Override
public void lostOwnership(Clipboard clipboard, Transferable contents)
{
if (!internalCopy)
internalCopy = false;
}
+ @Override
public void dragEnter(DropTargetDragEvent evt)
{
}
+ @Override
public void dragExit(DropTargetEvent evt)
{
}
+ @Override
public void dragOver(DropTargetDragEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void drop(DropTargetDropEvent evt)
{
boolean success = true;
}
else
{
- format = new IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
new FileLoader().LoadFile(file, protocol, format);
}
else
{
- format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
+ format = new IdentifyFile().identify(choice, FormatAdapter.FILE);
}
if (viewport != null)
}
else
{
- String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+ String format = new IdentifyFile().identify(url, FormatAdapter.URL);
if (format.equals("URL NOT FOUND"))
{
// message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
+ @Override
public void run()
{
new SplashScreen(true);
new Thread(new Runnable()
{
+ @Override
public void run()
{
// TODO: refactor to Jalview desktop session controller action.
selectedFile.getParent());
new Thread(new Runnable()
{
+ @Override
public void run()
{
setProgressBar(
sessit.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
if (dsktp.v_client == null)
Thread rthr = new Thread(new Runnable()
{
+ @Override
public void run()
{
dsktp.v_client = new VamsasApplication(dsktp, mysesid);
return showMemoryUsage;
}
+ @Override
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
groovyShell.setText(MessageManager.getString("label.groovy_console"));
groovyShell.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
groovyShell_actionPerformed();
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
if (progressBars == null)
* @see jalview.gui.IProgressIndicator#registerHandler(long,
* jalview.gui.IProgressIndicatorHandler)
*/
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
// only run if we aren't already displaying one of these.
addDialogThread(serviceChangedDialog = new Runnable()
{
+ @Override
public void run()
{
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
{
dialogExecutor.submit(new Runnable()
{
+ @Override
public void run()
{
if (dialogPause)
ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
"View of Desktop", getWidth(), getHeight(), of = new File(
"Jalview_snapshot" + System.currentTimeMillis()
- + ".eps"), "View of desktop");
+ + ".eps"), "View of desktop", null, 0, false);
try
{
paintAll(im.getGraphics());
git://source.jalview.org / jalview.git / commitdiff