From 10e637daad8983c41db8679baabea5563d7371f4 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 26 Mar 2015 09:57:03 +0000 Subject: [PATCH] JAL-1688 compiler warnings removed --- src/jalview/bin/Jalview.java | 36 +- src/jalview/gui/Desktop.java | 518 +++++++++++++++-------- src/jalview/gui/RestInputParamEditDialog.java | 4 +- src/jalview/ws/rest/RestServiceDescription.java | 160 +------ src/jalview/ws/seqfetcher/ASequenceFetcher.java | 36 +- 5 files changed, 403 insertions(+), 351 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 5bb5e98..0fe1664 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,13 +20,6 @@ */ package jalview.bin; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.io.HtmlSvgOutput; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.ws.jws2.Jws2Discoverer; - import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.BufferedReader; @@ -45,13 +38,20 @@ import java.security.CodeSource; import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; -import java.util.Hashtable; +import java.util.HashMap; import java.util.Map; import java.util.Vector; import javax.swing.UIManager; import javax.swing.UnsupportedLookAndFeelException; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.io.HtmlSvgOutput; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; + /** * Main class for Jalview Application
*
@@ -820,7 +820,7 @@ public class Jalview * = new Binding(); binding.setVariable("input", "world"); * gse.run("hello.groovy", binding); */ - Class[] bspec; + Class[] bspec; Object[] binding; int blen = ((jalviewContext[0] == null) ? 0 : 1) + ((jalviewContext[1] == null) ? 0 : 1); @@ -830,7 +830,7 @@ public class Jalview binding = new Object[blen * 2]; blen = 0; ClassLoader cl = null; - Map vbinding = new Hashtable(); + Map vbinding = new HashMap(); for (int jc = 0; jc < jalviewContext.length; jc++) { if (jalviewContext[jc] != null) @@ -847,8 +847,8 @@ public class Jalview blen++; } } - Class gbindingc = cl.loadClass("groovy.lang.Binding"); - Constructor gbcons; + Class gbindingc = cl.loadClass("groovy.lang.Binding"); + Constructor gbcons; Object gbinding; try { @@ -858,15 +858,15 @@ public class Jalview { // old style binding config - using series of string/object values to // setVariable. - gbcons = gbindingc.getConstructor(null); - gbinding = gbcons.newInstance(null); + gbcons = gbindingc.getConstructor(); + gbinding = gbcons.newInstance(); java.lang.reflect.Method setvar = gbindingc.getMethod( "setVariable", bspec); setvar.invoke(gbinding, binding); } - ; - Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); - Constructor gseccons = gsec.getConstructor(new Class[] + + Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); + Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class }); // String[].class }); Object gse = gseccons.newInstance(new Object[] { new URL[] @@ -966,7 +966,7 @@ public class Jalview private static FeatureFetcher startFeatureFetching(final Vector dasSources) { FeatureFetcher ff = new FeatureFetcher(); - AlignFrame afs[] = Desktop.getAlignframes(); + AlignFrame afs[] = Desktop.getAlignFrames(); if (afs == null || afs.length == 0) { return null; diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 3f3950c..db5bbe5 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,18 +20,6 @@ */ package jalview.gui; -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.GStructureViewer; -import jalview.structure.StructureSelectionManager; -import jalview.util.ImageMaker; -import jalview.util.MessageManager; -import jalview.ws.params.ParamManager; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -69,6 +57,7 @@ import java.lang.reflect.Constructor; import java.net.URL; import java.util.ArrayList; import java.util.Hashtable; +import java.util.List; import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.ExecutorService; @@ -95,6 +84,22 @@ import javax.swing.event.HyperlinkEvent.EventType; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +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; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.params.ParamManager; + /** * Jalview Desktop * @@ -162,6 +167,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements static final int yOffset = 30; + private static final int THREE = 3; + public static jalview.ws.jws1.Discoverer discoverer; public static Object[] jalviewClipboard; @@ -330,8 +337,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements + 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") + " " @@ -432,9 +438,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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 { @@ -480,7 +487,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); @@ -648,7 +657,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements addInternalFrame(frame, title, true, w, h, true); } - /** * Add an internal frame to the Jalview desktop * @@ -1087,7 +1095,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (format.equals("URL NOT FOUND")) { JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.couldnt_locate", new String[]{url}), MessageManager.getString("label.url_not_found"), + MessageManager.formatMessage("label.couldnt_locate", + new Object[] + { url }), MessageManager + .getString("label.url_not_found"), JOptionPane.WARNING_MESSAGE); return; @@ -1190,8 +1201,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (shortv) { message.append("

Version: " - + jalview.bin.Cache.getProperty("VERSION") - + "

"); + + jalview.bin.Cache.getProperty("VERSION") + ""); message.append("Last Updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + ""); @@ -1237,8 +1247,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } message.append("
Authors: " + jalview.bin.Cache - .getDefault( - "AUTHORFNAMES", + .getDefault("AUTHORFNAMES", "The Jalview Authors (See AUTHORS file for current list)") + "

Development managed by The Barton Group, University of Dundee, Scotland, UK.
" + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list" @@ -1363,7 +1372,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return; } - AlignViewport source = null, target = null; + AlignmentViewport source = null, target = null; if (frames[0] instanceof AlignFrame) { source = ((AlignFrame) frames[0]).getCurrentView(); @@ -1475,8 +1484,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void run() { - setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new String[]{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 @@ -1493,10 +1503,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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 String[]{ 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()); @@ -1564,13 +1575,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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 String[]{choice}), - choice.hashCode()); + setProgressBar(MessageManager.formatMessage( + "label.loading_jalview_project", new Object[] + { choice }), choice.hashCode()); try { new Jalview2XML().loadJalviewAlign(choice); @@ -1581,9 +1594,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.error("Problems whilst loading project from " + choice, ex); - JOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.error_whilst_loading_project_from", new String[]{choice}), - MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE); + JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + .formatMessage( + "label.error_whilst_loading_project_from", + new Object[] + { choice }), MessageManager + .getString("label.couldnt_load_project"), + JOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1604,7 +1621,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (fileLoadingCount == 0) { - fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName}))); + fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage( + "label.loading_file", new Object[] + { fileName }))); } fileLoadingCount++; } @@ -1670,38 +1689,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements public static int getViewCount(String alignmentId) { - AlignViewport[] aps = getViewports(alignmentId); + AlignmentViewport[] aps = getViewports(alignmentId); return (aps == null) ? 0 : aps.length; } /** * * @param alignmentId + * - if null, all sets are returned * @return all AlignmentPanels concerning the alignmentId sequence set */ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { - int count = 0; if (Desktop.desktop == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode return null; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - ArrayList aps = new ArrayList(); - for (int t = 0; t < frames.length; t++) + List aps = new ArrayList(); + AlignFrame[] frames = getAlignFrames(); + if (frames == null) { - if (frames[t] instanceof AlignFrame) + return null; + } + for (AlignFrame af : frames) + { + for (AlignmentPanel ap : af.alignPanels) { - AlignFrame af = (AlignFrame) frames[t]; - for (int a = 0; a < af.alignPanels.size(); a++) + if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId())) { - if (alignmentId.equals(((AlignmentPanel) af.alignPanels - .elementAt(a)).av.getSequenceSetId())) - { - aps.add(af.alignPanels.elementAt(a)); - } + aps.add(ap); } } } @@ -1709,11 +1727,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - AlignmentPanel[] vap = new AlignmentPanel[aps.size()]; - for (int t = 0; t < vap.length; t++) - { - vap[t] = (AlignmentPanel) aps.get(t); - } + AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); return vap; } @@ -1721,52 +1735,51 @@ public class Desktop extends jalview.jbgui.GDesktop implements * get all the viewports on an alignment. * * @param sequenceSetId - * unique alignment id + * unique alignment id (may be null - all viewports returned in that + * case) * @return all viewports on the alignment bound to sequenceSetId */ - public static AlignViewport[] getViewports(String sequenceSetId) + public static AlignmentViewport[] getViewports(String sequenceSetId) { - Vector viewp = new Vector(); + List viewp = new ArrayList(); if (desktop != null) { - javax.swing.JInternalFrame[] frames = instance.getAllFrames(); + AlignFrame[] frames = Desktop.getAlignFrames(); - for (int t = 0; t < frames.length; t++) + for (AlignFrame afr : frames) { - if (frames[t] instanceof AlignFrame) + if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) { - AlignFrame afr = ((AlignFrame) frames[t]); - if (afr.getViewport().getSequenceSetId().equals(sequenceSetId)) + if (afr.alignPanels != null) { - if (afr.alignPanels != null) + for (AlignmentPanel ap : afr.alignPanels) { - for (int a = 0; a < afr.alignPanels.size(); a++) + if (sequenceSetId == null + || sequenceSetId.equals(ap.av.getSequenceSetId())) { - if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels - .elementAt(a)).av.getSequenceSetId())) - { - viewp.addElement(((AlignmentPanel) afr.alignPanels - .elementAt(a)).av); - } + viewp.add(ap.av); } } - else - { - viewp.addElement(((AlignFrame) frames[t]).getViewport()); - } + } + else + { + viewp.add(afr.getViewport()); } } } if (viewp.size() > 0) { - AlignViewport[] vp = new AlignViewport[viewp.size()]; - viewp.copyInto(vp); - return vp; + return viewp.toArray(new AlignmentViewport[viewp.size()]); } } return null; } + /** + * Explode the views in the given frame into separate AlignFrame + * + * @param af + */ public void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); @@ -1777,15 +1790,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (int i = 0; i < size; i++) { - AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i); + 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); @@ -1796,10 +1815,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements } + /** + * 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(); @@ -1811,12 +1838,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements boolean gatherThis = false; for (int a = 0; a < af.alignPanels.size(); a++) { - AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a); + AlignmentPanel ap = af.alignPanels.get(a); 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); } } @@ -1842,7 +1869,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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")); @@ -1858,7 +1886,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Desktop.desktop, MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", - new String[] + new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), @@ -1935,23 +1963,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements return false; } - setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{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 String[]{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 String[]{file.getName()}), - file.hashCode()); + setProgressBar(MessageManager.formatMessage( + "status.importing_vamsas_session_from", new Object[] + { file.getName() }), file.hashCode()); return v_client.inSession(); } @@ -1959,11 +1990,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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(); @@ -2053,7 +2087,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); sessit.setToolTipText(MessageManager.formatMessage( - "label.connect_to_session", new String[] + "label.connect_to_session", new Object[] { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; @@ -2110,14 +2144,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements { "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 String[]{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; @@ -2169,7 +2206,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } 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); @@ -2204,6 +2242,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements public class MyDesktopPane extends JDesktopPane implements Runnable { + private static final float ONE_MB = 1048576f; + boolean showMemoryUsage = false; Runtime runtime; @@ -2243,9 +2283,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { try { - maxMemory = runtime.maxMemory() / 1048576f; - allocatedMemory = runtime.totalMemory() / 1048576f; - freeMemory = runtime.freeMemory() / 1048576f; + maxMemory = runtime.maxMemory() / ONE_MB; + allocatedMemory = runtime.totalMemory() / ONE_MB; + freeMemory = runtime.freeMemory() / ONE_MB; totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); percentUsage = (totalFreeMemory / maxMemory) * 100; @@ -2279,7 +2319,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { g.drawString(MessageManager.formatMessage( "label.memory_stats", - new String[] + new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }), 10, getHeight() - fm.getHeight()); @@ -2319,8 +2359,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Accessor method to quickly get all the AlignmentFrames loaded. + * + * @return an array of AlignFrame, or null if none found */ - public static AlignFrame[] getAlignframes() + public static AlignFrame[] getAlignFrames() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -2328,35 +2370,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - Vector avp = new Vector(); - try + List avp = new ArrayList(); + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) { - // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + if (frames[i] instanceof AlignFrame) { - if (frames[i] instanceof AlignFrame) + avp.add((AlignFrame) frames[i]); + } + else if (frames[i] instanceof SplitFrame) + { + /* + * Also check for a split frame containing an AlignFrame + */ + GSplitFrame sf = (GSplitFrame) frames[i]; + if (sf.getTopFrame() instanceof AlignFrame) + { + avp.add((AlignFrame) sf.getTopFrame()); + } + if (sf.getBottomFrame() instanceof AlignFrame) { - AlignFrame af = (AlignFrame) frames[i]; - avp.addElement(af); + avp.add((AlignFrame) sf.getBottomFrame()); } } - } catch (Exception ex) - { - ex.printStackTrace(); } if (avp.size() == 0) { return null; } - AlignFrame afs[] = new AlignFrame[avp.size()]; - for (int i = 0, j = avp.size(); i < j; i++) - { - afs[i] = (AlignFrame) avp.elementAt(i); - } - avp.clear(); + AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]); return afs; } + /** + * Returns an array of any AppJmol frames in the Desktop (or null if none). + * + * @return + */ public GStructureViewer[] getJmols() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -2365,32 +2415,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - Vector avp = new Vector(); - try + List avp = new ArrayList(); + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) { - // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + if (frames[i] instanceof AppJmol) { - if (frames[i] instanceof AppJmol) - { - GStructureViewer af = (GStructureViewer) frames[i]; - avp.addElement(af); - } + GStructureViewer af = (GStructureViewer) frames[i]; + avp.add(af); } - } catch (Exception ex) - { - ex.printStackTrace(); } if (avp.size() == 0) { return null; } - GStructureViewer afs[] = new GStructureViewer[avp.size()]; - for (int i = 0, j = avp.size(); i < j; i++) - { - afs[i] = (GStructureViewer) avp.elementAt(i); - } - avp.clear(); + GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]); return afs; } @@ -2402,31 +2441,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements // 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 { - Class gcClass = Desktop.class.getClassLoader().loadClass( + Class gcClass = Desktop.class.getClassLoader().loadClass( "groovy.ui.Console"); - Constructor gccons = gcClass.getConstructor(null); + Constructor gccons = gcClass.getConstructor(); java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class }); - java.lang.reflect.Method run = gcClass.getMethod("run", null); - Object gc = gccons.newInstance(null); + java.lang.reflect.Method run = gcClass.getMethod("run"); + Object gc = gccons.newInstance(); setvar.invoke(gc, new Object[] { "Jalview", this }); - run.invoke(gc, null); + run.invoke(gc); } 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); } } @@ -2476,7 +2515,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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)); @@ -2491,7 +2532,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((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); @@ -2513,20 +2557,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * This will return the first AlignFrame viewing AlignViewport av. It will - * break if there are more than one AlignFrames viewing a particular av. This + * 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 av - * @return alignFrame for av + * @param viewport + * @return alignFrame for viewport */ - public static AlignFrame getAlignFrameFor(AlignViewport av) + public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { if (desktop != null) { - AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId()); + AlignmentPanel[] aps = getAlignmentPanels(viewport + .getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { - if (aps[panel] != null && aps[panel].av == av) + if (aps[panel] != null && aps[panel].av == viewport) { return aps[panel].alignFrame; } @@ -2753,17 +2798,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progress != null) { - progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new String[]{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(); } @@ -2878,6 +2924,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements dialogPause = false; block.release(); } + @Override protected void snapShotWindow_actionPerformed(ActionEvent e) { @@ -2887,14 +2934,139 @@ public class Desktop extends jalview.jbgui.GDesktop implements "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 topPanels = oldTopFrame + .getAlignPanels(); + List 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); + } } diff --git a/src/jalview/gui/RestInputParamEditDialog.java b/src/jalview/gui/RestInputParamEditDialog.java index 6078377..9a71770 100644 --- a/src/jalview/gui/RestInputParamEditDialog.java +++ b/src/jalview/gui/RestInputParamEditDialog.java @@ -50,7 +50,7 @@ public class RestInputParamEditDialog extends GRestInputParamEditDialog try { return (InputType) (typeclass.get(name).getConstructor() - .newInstance(null)); + .newInstance()); } catch (Throwable x) { System.err @@ -187,7 +187,7 @@ public class RestInputParamEditDialog extends GRestInputParamEditDialog { JPanel inopts = new JPanel(new MigLayout()); ArrayList opts = new ArrayList(), prms = new ArrayList(); - jtype = (InputType) (type.getConstructor().newInstance(null)); + jtype = (InputType) (type.getConstructor().newInstance()); typeclass.put(jtype.getURLtokenPrefix(), type); // and populate parameters from this type OptsAndParamsPage opanp = new OptsAndParamsPage(this, true); diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java index 177ebb8..e7c861f 100644 --- a/src/jalview/ws/rest/RestServiceDescription.java +++ b/src/jalview/ws/rest/RestServiceDescription.java @@ -20,12 +20,6 @@ */ package jalview.ws.rest; -import jalview.datamodel.SequenceI; -import jalview.io.packed.DataProvider.JvDataType; -import jalview.ws.rest.params.Alignment; -import jalview.ws.rest.params.AnnotationFile; -import jalview.ws.rest.params.SeqGroupIndexVector; - import java.net.URL; import java.util.ArrayList; import java.util.HashMap; @@ -37,8 +31,17 @@ import java.util.StringTokenizer; import java.util.regex.Matcher; import java.util.regex.Pattern; +import jalview.datamodel.SequenceI; +import jalview.io.packed.DataProvider.JvDataType; +import jalview.util.StringUtils; +import jalview.ws.rest.params.Alignment; +import jalview.ws.rest.params.AnnotationFile; +import jalview.ws.rest.params.SeqGroupIndexVector; + public class RestServiceDescription { + private static final Pattern PARAM_ENCODED_URL_PATTERN = Pattern.compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$"); + /** * create a new rest service description ready to be configured */ @@ -77,6 +80,7 @@ public class RestServiceDescription this.gapCharacter = gapCharacter; } + @Override public boolean equals(Object o) { if (o == null || !(o instanceof RestServiceDescription)) @@ -87,7 +91,8 @@ public class RestServiceDescription boolean diff = (gapCharacter != other.gapCharacter); diff |= vseparable != other.vseparable; diff |= hseparable != other.hseparable; - diff |= !(urlSuffix.equals(other.urlSuffix)); + diff |= !(urlSuffix == null && other.urlSuffix == null || (urlSuffix != null + && other.urlSuffix != null && urlSuffix.equals(other.urlSuffix))); // TODO - robust diff that includes constants and reordering of URL // diff |= !(postUrl.equals(other.postUrl)); // diff |= !inputParams.equals(other.inputParams); @@ -356,131 +361,6 @@ public class RestServiceDescription return invalidMessage == null; } - private static boolean debug = false; - - /** - * parse the string into a list - * - * @param list - * @param separator - * @return elements separated by separator - */ - public static String[] separatorListToArray(String list, String separator) - { - int seplen = separator.length(); - if (list == null || list.equals("") || list.equals(separator)) - return null; - java.util.ArrayList jv = new ArrayList(); - int cp = 0, pos, escape; - boolean wasescaped = false, wasquoted = false; - String lstitem = null; - while ((pos = list.indexOf(separator, cp)) >= cp) - { - - escape = (pos > 0 && list.charAt(pos - 1) == '\\') ? -1 : 0; - if (wasescaped || wasquoted) - { - // append to previous pos - jv.set(jv.size() - 1, - lstitem = lstitem + separator - + list.substring(cp, pos + escape)); - - } - else - { - jv.add(lstitem = list.substring(cp, pos + escape)); - } - cp = pos + seplen; - wasescaped = escape == -1; - if (!wasescaped) - { - // last separator may be in an unmatched quote - if (java.util.regex.Pattern.matches("('[^']*')*[^']*'", lstitem)) - { - wasquoted = true; - } - } - - } - if (cp < list.length()) - { - String c = list.substring(cp); - if (wasescaped || wasquoted) - { - // append final separator - jv.set(jv.size() - 1, lstitem + separator + c); - } - else - { - if (!c.equals(separator)) - { - jv.add(c); - } - } - } - if (jv.size() > 0) - { - String[] v = jv.toArray(new String[jv.size()]); - jv.clear(); - if (debug) - { - System.err.println("Array from '" + separator - + "' separated List:\n" + v.length); - for (int i = 0; i < v.length; i++) - { - System.err.println("item " + i + " '" + v[i] + "'"); - } - } - return v; - } - if (debug) - { - System.err.println("Empty Array from '" + separator - + "' separated List"); - } - return null; - } - - /** - * concatenate the list with separator - * - * @param list - * @param separator - * @return concatenated string - */ - public static String arrayToSeparatorList(String[] list, String separator) - { - StringBuffer v = new StringBuffer(); - if (list != null && list.length > 0) - { - for (int i = 0, iSize = list.length; i < iSize; i++) - { - if (list[i] != null) - { - if (v.length() > 0) - { - v.append(separator); - } - // TODO - escape any separator values in list[i] - v.append(list[i]); - } - } - if (debug) - { - System.err.println("Returning '" + separator - + "' separated List:\n"); - System.err.println(v); - } - return v.toString(); - } - if (debug) - { - System.err.println("Returning empty '" + separator - + "' separated List\n"); - } - return "" + separator; - } - /** * parse a string containing a list of service properties and configure the * service description @@ -492,7 +372,7 @@ public class RestServiceDescription private boolean configureFromServiceInputProperties(String propList, StringBuffer warnings) { - String[] props = separatorListToArray(propList, ","); + String[] props = StringUtils.separatorListToArray(propList, ","); if (props == null) { return true; @@ -610,7 +490,7 @@ public class RestServiceDescription ; vls.add(new String("gapCharacter='" + gapCharacter + "'")); vls.add(new String("returns='" + _genOutputFormatString() + "'")); - return arrayToSeparatorList(vls.toArray(new String[0]), ","); + return StringUtils.arrayToSeparatorList(vls.toArray(new String[0]), ","); } public String toString() @@ -653,7 +533,7 @@ public class RestServiceDescription public boolean configureFromEncodedString(String encoding, StringBuffer warnings) { - String[] list = separatorListToArray(encoding, "|"); + String[] list = StringUtils.separatorListToArray(encoding, "|"); int nextpos = parseServiceList(list, warnings, 0); if (nextpos > 0) @@ -754,7 +634,7 @@ public class RestServiceDescription url.append("$"); url.append(param.getValue().getURLtokenPrefix()); url.append(":"); - url.append(arrayToSeparatorList(vals.toArray(new String[0]), + url.append(StringUtils.arrayToSeparatorList(vals.toArray(new String[0]), ",")); url.append("$"); } @@ -781,7 +661,7 @@ public class RestServiceDescription boolean valid = true; int lastp = 0; String url = new String(); - Matcher prms = Pattern.compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$") + Matcher prms = PARAM_ENCODED_URL_PATTERN .matcher(ipurl); Map iparams = new Hashtable(); InputType jinput; @@ -843,11 +723,11 @@ public class RestServiceDescription { try { - jinput = (InputType) (type.getConstructor().newInstance(null)); + jinput = (InputType) (type.getConstructor().newInstance()); if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix())) { ArrayList al = new ArrayList(); - for (String prprm : separatorListToArray(iprmparams, ",")) + for (String prprm : StringUtils.separatorListToArray(iprmparams, ",")) { // hack to ensure that strings like "sep=','" containing unescaped // commas as values are concatenated @@ -998,7 +878,7 @@ public class RestServiceDescription public static List parseDescriptions( String services) throws Exception { - String[] list = separatorListToArray(services, "|"); + String[] list = StringUtils.separatorListToArray(services, "|"); List svcparsed = new ArrayList(); int p = 0, lastp = 0; StringBuffer warnings = new StringBuffer(); diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java index 7dbda90..a8a3904 100644 --- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java +++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java @@ -20,12 +20,6 @@ */ package jalview.ws.seqfetcher; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.SequenceI; -import jalview.util.DBRefUtils; -import jalview.util.MessageManager; - import java.util.ArrayList; import java.util.Enumeration; import java.util.HashSet; @@ -36,6 +30,12 @@ import java.util.Map; import java.util.Stack; import java.util.Vector; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.SequenceI; +import jalview.util.DBRefUtils; +import jalview.util.MessageManager; + public class ASequenceFetcher { @@ -58,7 +58,9 @@ public class ASequenceFetcher public String[] getSupportedDb() { if (FETCHABLEDBS == null) + { return null; + } String[] sf = new String[FETCHABLEDBS.size()]; Enumeration e = FETCHABLEDBS.keys(); int i = 0; @@ -77,7 +79,9 @@ public class ASequenceFetcher { String db = (String) e.nextElement(); if (source.compareToIgnoreCase(db) == 0) + { return true; + } } jalview.bin.Cache.log.warn("isFetchable doesn't know about '" + source + "'"); @@ -198,7 +202,9 @@ public class ASequenceFetcher */ System.out.println(hdr); if (rrb != null) + { System.out.println(rrb); + } System.out.println("# end of " + hdr); } @@ -303,24 +309,16 @@ public class ASequenceFetcher * @param dbSourceProxy * reference for class implementing * jalview.ws.seqfetcher.DbSourceProxy - * @throws java.lang.IllegalArgumentException - * if class does not implement jalview.ws.seqfetcher.DbSourceProxy */ - protected void addDBRefSourceImpl(Class dbSourceProxy) + protected void addDBRefSourceImpl( + Class dbSourceProxy) throws java.lang.IllegalArgumentException { DbSourceProxy proxy = null; try { - Object proxyObj = dbSourceProxy.getConstructor(null) - .newInstance(null); - if (!DbSourceProxy.class.isInstance(proxyObj)) - { - throw new IllegalArgumentException( - dbSourceProxy.toString() - + " does not implement the jalview.ws.seqfetcher.DbSourceProxy"); - } - proxy = (DbSourceProxy) proxyObj; + DbSourceProxy proxyObj = dbSourceProxy.getConstructor().newInstance(); + proxy = proxyObj; } catch (IllegalArgumentException e) { throw e; @@ -426,6 +424,7 @@ public class ASequenceFetcher { ArrayList prlist = new ArrayList(); for (String fetchable : getSupportedDb()) + { for (DbSourceProxy pr : getSourceProxy(fetchable)) { if (class1.isInstance(pr)) @@ -433,6 +432,7 @@ public class ASequenceFetcher prlist.add(pr); } } + } if (prlist.size() == 0) { return null; -- 1.7.10.2