package jalview.gui;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
import jalview.util.ImageMaker;
+ jalview.bin.Cache.getProperty("VERSION") + "\n"
+ "Jalview Installation: "
+ jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
- + "\n"
- + "Build Date: "
+ + "\n" + "Build Date: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+ "Java version: " + System.getProperty("java.version") + "\n"
+ System.getProperty("os.arch") + " "
{
ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
- ssm.setSecStructServices(jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW,
- true));
+ ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(
+ Preferences.STRUCT_FROM_PDB, true));
+ ssm.setSecStructServices(jalview.bin.Cache.getDefault(
+ Preferences.USE_RNAVIEW, true));
}
else
{
public void run()
{
long instance = System.currentTimeMillis();
- Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), instance);
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"),
+ instance);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, instance);
jvnews.showNews();
addInternalFrame(frame, title, true, w, h, true);
}
-
/**
* Add an internal frame to the Jalview desktop
*
if (shortv)
{
message.append("<h1><strong>Version: "
- + jalview.bin.Cache.getProperty("VERSION")
- + "</strong></h1>");
+ + jalview.bin.Cache.getProperty("VERSION") + "</strong></h1>");
message.append("<strong>Last Updated: <em>"
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ "</em></strong>");
}
message.append("<br>Authors: "
+ jalview.bin.Cache
- .getDefault(
- "AUTHORFNAMES",
+ .getDefault("AUTHORFNAMES",
"The Jalview Authors (See AUTHORS file for current list)")
+ "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
public void run()
{
- setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new Object[]{choice.getName()}),
- choice.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "label.saving_jalview_project", new Object[]
+ { choice.getName() }), choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
choice.getParent());
// TODO catch and handle errors for savestate
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JOptionPane.showMessageDialog(
- me,
- MessageManager.formatMessage("label.error_whilst_saving_current_state_to", new Object[]{ choice.getName()}),
- MessageManager.getString("label.couldnt_save_project"),
+ JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[]
+ { choice.getName() }), MessageManager
+ .getString("label.couldnt_save_project"),
JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
final File selectedFile = chooser.getSelectedFile();
setProjectFile(selectedFile);
final String choice = selectedFile.getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ selectedFile.getParent());
new Thread(new Runnable()
{
public void run()
{
setProgressBar(MessageManager.formatMessage(
"label.loading_jalview_project", new Object[]
- { choice }),
- choice.hashCode());
+ { choice }), choice.hashCode());
try
{
new Jalview2XML().loadJalviewAlign(choice);
{
Cache.log.error("Problems whilst loading project from "
+ choice, ex);
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage(
"label.error_whilst_loading_project_from",
new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE);
+ { choice }), MessageManager
+ .getString("label.couldnt_load_project"),
+ JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
aps.add(ap);
}
}
- // for (int a = 0; a < af.alignPanels.size(); a++)
- // {
- // if (alignmentId.equals(af.alignPanels
- // .get(a).av.getSequenceSetId()))
- // {
- // aps.add(af.alignPanels.get(a));
- // }
- // }
}
if (aps.size() == 0)
{
return null;
}
+ /**
+ * Explode the views in the given frame into separate AlignFrame
+ *
+ * @param af
+ */
public void explodeViews(AlignFrame af)
{
int size = af.alignPanels.size();
{
AlignmentPanel ap = af.alignPanels.get(i);
AlignFrame newaf = new AlignFrame(ap);
- if (ap.av.explodedPosition != null
- && !ap.av.explodedPosition.equals(af.getBounds()))
+
+ /*
+ * Restore the view's last exploded frame geometry if known. Multiple
+ * views from one exploded frame share and restore the same (frame)
+ * position and size.
+ */
+ Rectangle geometry = ap.av.getExplodedGeometry();
+ if (geometry != null)
{
- newaf.setBounds(ap.av.explodedPosition);
+ newaf.setBounds(geometry);
}
- ap.av.gatherViewsHere = false;
+ ap.av.setGatherViewsHere(false);
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
+ /**
+ * Gather expanded views (separate AlignFrame's) with the same sequence set
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
+ *
+ * @param source
+ */
public void gatherViews(AlignFrame source)
{
- source.viewport.gatherViewsHere = true;
- source.viewport.explodedPosition = source.getBounds();
+ source.viewport.setGatherViewsHere(true);
+ source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
if (viewId.equals(ap.av.getSequenceSetId()))
{
gatherThis = true;
- ap.av.gatherViewsHere = false;
- ap.av.explodedPosition = af.getBounds();
+ ap.av.setGatherViewsHere(false);
+ ap.av.setExplodedGeometry(af.getBounds());
source.addAlignmentPanel(ap, false);
}
}
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.open_saved_vamsas_session"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.open_saved_vamsas_session"));
chooser.setToolTipText(MessageManager
.getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
return false;
}
- setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new Object[]{file.getName()}),
- file.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
try
{
v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
- setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new Object[]{file.getName()}),
- file.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
jalview.bin.Cache.log.error(
"New vamsas session from existing session file failed:", ex);
return false;
}
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
- setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new Object[]{file.getName()}),
- file.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
return v_client.inSession();
}
{
if (v_client != null)
{
- throw new Error(MessageManager.getString("error.try_join_vamsas_session_another"));
+ throw new Error(
+ MessageManager
+ .getString("error.try_join_vamsas_session_another"));
}
if (mysesid == null)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_session_id"));
+ throw new Error(
+ MessageManager.getString("error.invalid_vamsas_session_id"));
}
v_client = new VamsasApplication(this, mysesid);
setupVamsasConnectedGui();
{ "Vamsas Document" }, "Vamsas Document");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_vamsas_document_archive"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_vamsas_document_archive"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager.formatMessage("label.saving_vamsas_doc", new Object[]{choice.getName()}));
+ JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
+ "label.saving_vamsas_doc", new Object[]
+ { choice.getName() }));
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
}
if (b)
{
- vamUpdate = this.addProgressPanel(MessageManager.getString("label.updating_vamsas_session"));
+ vamUpdate = this.addProgressPanel(MessageManager
+ .getString("label.updating_vamsas_session"));
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
/*
* Also check for a split frame containing an AlignFrame
*/
- SplitFrame sf = (SplitFrame) frames[i];
- if (sf.getTopComponent() instanceof AlignFrame)
+ GSplitFrame sf = (GSplitFrame) frames[i];
+ if (sf.getTopFrame() instanceof AlignFrame)
{
- avp.add((AlignFrame) sf.getTopComponent());
+ avp.add((AlignFrame) sf.getTopFrame());
}
- if (sf.getBottomComponent() instanceof AlignFrame)
+ if (sf.getBottomFrame() instanceof AlignFrame)
{
- avp.add((AlignFrame) sf.getBottomComponent());
+ avp.add((AlignFrame) sf.getBottomFrame());
}
}
}
// use reflection to avoid creating compilation dependency.
if (!jalview.bin.Cache.groovyJarsPresent())
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_create_groovyshell"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_create_groovyshell"));
}
try
{
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.couldnt_create_groovy_shell"),
- MessageManager.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JOptionPane.ERROR_MESSAGE);
}
}
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+ throw new Error(
+ MessageManager
+ .getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = progressBars.get(new Long(id));
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new Object[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+ us.setProgressBar(MessageManager.formatMessage(
+ "label.cancelled_params", new Object[]
+ { ((JLabel) progressPanel.getComponent(0)).getText() }),
+ id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
}
/**
- * This will return the AlignFrame holding the given viewport instance. It
+ * This will return the first AlignFrame holding the given viewport instance. It
* will break if there are more than one AlignFrames viewing a particular av.
*
* @param viewport
{
if (progress != null)
{
- progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new Object[]{url}), this.hashCode());
+ progress.setProgressBar(MessageManager.formatMessage(
+ "status.opening_params", new Object[]
+ { url }), this.hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
dialogPause = false;
block.release();
}
+
@Override
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
"View of Desktop", getWidth(), getHeight(), of = new File(
"Jalview_snapshot" + System.currentTimeMillis()
+ ".eps"), "View of desktop");
- try {
+ try
+ {
paintAll(im.getGraphics());
im.writeImage();
} catch (Exception q)
{
- Cache.log.error("Couldn't write snapshot to "+of.getAbsolutePath(),q);
+ Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
+ q);
+ return;
+ }
+ Cache.log.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+
+ /**
+ * Explode the views in the given frame into separate AlignFrame windows.
+ *
+ * @param sf
+ */
+ public void explodeViews(SplitFrame sf)
+ {
+ AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
+ List<? extends AlignmentViewPanel> topPanels = oldTopFrame
+ .getAlignPanels();
+ List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
+ .getAlignPanels();
+ int viewCount = topPanels.size();
+ if (viewCount < 2)
+ {
return;
}
- Cache.log.info("Successfully written snapshot to file "+of.getAbsolutePath());
+
+ /*
+ * Processing in reverse order works, forwards order leaves the first panels
+ * not visible. I don't know why!
+ */
+ for (int i = viewCount - 1; i >= 0; i--)
+ {
+ /*
+ * Make new top and bottom frames. These take over the respective
+ * AlignmentPanel objects, including their AlignmentViewports, so the
+ * cdna/protein relationships between the viewports is carried over to the
+ * new split frames.
+ */
+ AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
+ AlignFrame newTopFrame = new AlignFrame(topPanel);
+ newTopFrame.setVisible(true);
+ AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
+ AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
+ newBottomFrame.setVisible(true);
+ topPanel.av.setGatherViewsHere(false);
+ bottomPanel.av.setGatherViewsHere(false);
+ JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+ newBottomFrame);
+ // either panel may hold previous exploded frame geometry
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ splitFrame.setBounds(geometry);
+ }
+ Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
+ }
+
+ /*
+ * Clear references to the panels (now relocated in the new SplitFrames)
+ * before closing the old SplitFrame.
+ */
+ topPanels.clear();
+ bottomPanels.clear();
+ sf.close();
+ }
+
+ /**
+ * Gather expanded split frames, sharing the same pairs of sequence set ids,
+ * back into the given SplitFrame as additional views. Note that the gathered
+ * frames may themselves have multiple views.
+ *
+ * @param source
+ */
+ public void gatherViews(GSplitFrame source)
+ {
+ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
+ AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
+ myTopFrame.viewport.setExplodedGeometry(source.getBounds());
+ myBottomFrame.viewport.setExplodedGeometry(source.getBounds());
+ myTopFrame.viewport.setGatherViewsHere(true);
+ myBottomFrame.viewport.setGatherViewsHere(true);
+ String topViewId = myTopFrame.viewport.getSequenceSetId();
+ String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
+
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof SplitFrame && frame != source)
+ {
+ SplitFrame sf = (SplitFrame) frame;
+ AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
+ boolean gatherThis = false;
+ for (int a = 0; a < topFrame.alignPanels.size(); a++)
+ {
+ AlignmentPanel topPanel = topFrame.alignPanels.get(a);
+ AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
+ if (topViewId.equals(topPanel.av.getSequenceSetId())
+ && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ topPanel.av.setGatherViewsHere(false);
+ bottomPanel.av.setGatherViewsHere(false);
+ // both panels refer to the same split frame geometry
+ Rectangle position = sf.getBounds();
+ topPanel.av.setExplodedGeometry(position);
+ bottomPanel.av.setExplodedGeometry(position);
+ myTopFrame.addAlignmentPanel(topPanel, false);
+ myBottomFrame.addAlignmentPanel(bottomPanel, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ topFrame.getAlignPanels().clear();
+ bottomFrame.getAlignPanels().clear();
+ sf.close();
+ }
+ }
+ }
+
+ /*
+ * The dust settles...give focus to the tab we did this from.
+ */
+ myTopFrame.setDisplayedView(myTopFrame.alignPanel);
+
}
}
git://source.jalview.org / jalview.git / blobdiff