From 4edc470836068d06d8033a849f7eec780d39eb99 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 6 Dec 2006 17:29:52 +0000 Subject: [PATCH] type change --- src/jalview/gui/VamsasClient.java | 180 ++++++++++++++++++------------------- 1 file changed, 87 insertions(+), 93 deletions(-) diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java index df6dbdd..b97e181 100755 --- a/src/jalview/gui/VamsasClient.java +++ b/src/jalview/gui/VamsasClient.java @@ -31,46 +31,46 @@ import org.vamsas.test.simpleclient.ClientDoc; * */ public class VamsasClient extends ArchiveClient { - // Cache.preferences for vamsas client session arena - // preferences for check for default session at startup. - // user and organisation stuff. - public VamsasClient(Desktop jdesktop, - File sessionPath) { - super(System.getProperty("user.name"),System.getProperty("host.name"), "jalview","2.7", - sessionPath); - } - public void initial_update() { - Cache.log.info("Jalview loading the Vamsas Session."); - // load in the vamsas archive for the first time - ClientDoc cdoc = this.getUpdateable(); - updateJalview(cdoc); + // Cache.preferences for vamsas client session arena + // preferences for check for default session at startup. + // user and organisation stuff. + public VamsasClient(Desktop jdesktop, + File sessionPath) { + super(System.getProperty("user.name"),System.getProperty("host.name"), "jalview","2.7", + sessionPath); + } + public void initial_update() { + Cache.log.info("Jalview loading the Vamsas Session."); + // load in the vamsas archive for the first time + ClientDoc cdoc = this.getUpdateable(); + updateJalview(cdoc); JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) { - return; + return; } try { //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; - af.alignPanel.alignmentChanged(); - } + AlignFrame af = (AlignFrame) frames[i]; + af.alignPanel.alignmentChanged(); } + } } catch (Exception e) { Cache.log.warn("Exception whilst refreshing jalview windows after a vamsas document update.", e); } doUpdate(cdoc); cdoc.closeDoc(); } - /** - * this will close all windows currently in Jalview. - * + /** + * this will close all windows currently in Jalview. + * protected void closeWindows() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -95,10 +95,10 @@ public class VamsasClient extends ArchiveClient { // Close windows - load update. Cache.log.info("Jalview updating from Vamsas Session."); } - */ + */ VamsasClientWatcher watcher=null; - public void push_update() { - watchForChange=false; + public void push_update() { + watchForChange=false; try { Thread.sleep(WATCH_SLEEP); } catch (Exception e) { @@ -111,20 +111,14 @@ public class VamsasClient extends ArchiveClient { cdoc=null; watchForChange=true; if (watcher!=null) { - Thread wthread = new Thread() { - public void run() { - watcher.run(); - } - }; - wthread.start(); - + watcher.start(); } - // collect all uncached alignments and put them into the vamsas dataset. - // store them. - Cache.log.info("Jalview updating the Vamsas Session."); - } - public void end_session() { - // stop any update/watcher thread. + // collect all uncached alignments and put them into the vamsas dataset. + // store them. + Cache.log.info("Jalview updating the Vamsas Session."); + } + public void end_session() { + // stop any update/watcher thread. watchForChange=false; // this makes any watch(long) loops return. // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped. try { @@ -133,90 +127,90 @@ public class VamsasClient extends ArchiveClient { }; Cache.log.info("Jalview disconnecting from the Vamsas Session."); - } - public void updateJalview(ClientDoc cdoc) { - ensureJvVamsas(); + } + public void updateJalview(ClientDoc cdoc) { + ensureJvVamsas(); VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry()); vds.updateToJalview(); - } - private void ensureJvVamsas() { + } + private void ensureJvVamsas() { if (jv2vobj==null) { jv2vobj = new IdentityHashMap(); vobj2jv = new Hashtable(); } - } - /** - * jalview object binding to VorbaIds - */ - IdentityHashMap jv2vobj = null; - Hashtable vobj2jv = null; - public void updateVamsasDocument(ClientDoc doc) { - ensureJvVamsas(); + } + /** + * jalview object binding to VorbaIds + */ + IdentityHashMap jv2vobj = null; + Hashtable vobj2jv = null; + public void updateVamsasDocument(ClientDoc doc) { + ensureJvVamsas(); VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, baseProvEntry()); // wander through frames - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - if (frames == null) - { - return; - } + if (frames == null) + { + return; + } - try + try + { + //REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) { - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) - { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; - - // update alignment and root from frame. - vds.storeVAMSAS(af.getViewport(), af.getTitle()); - } - } - } - catch (Exception e) { - Cache.log.error("Vamsas Document store exception",e); + AlignFrame af = (AlignFrame) frames[i]; + + // update alignment and root from frame. + vds.storeVAMSAS(af.getViewport(), af.getTitle()); } - } - private Entry baseProvEntry() { + } + } + catch (Exception e) { + Cache.log.error("Vamsas Document store exception",e); + } + } + private Entry baseProvEntry() { org.vamsas.objects.core.Entry pentry = new org.vamsas.objects.core.Entry(); pentry.setUser(this.getProvenanceUser()); pentry.setApp(this.getClientHandle().getClientName()); pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date())); pentry.setAction("created"); return pentry; - } - protected class VamsasClientWatcher extends Thread implements Runnable { - /* (non-Javadoc) - * @see java.lang.Thread#run() - */ - VamsasClient client=null; - VamsasClientWatcher(VamsasClient client) { - this.client = client; - } + } + protected class VamsasClientWatcher extends Thread { + /* (non-Javadoc) + * @see java.lang.Thread#run() + */ + VamsasClient client=null; + VamsasClientWatcher(VamsasClient client) { + this.client = client; + } boolean running=false; - public void run() { - running=true; - while (client.watchForChange) { - ClientDoc docio = client.watch(0); - if (docio!=null) { + public void run() { + running=true; + while (client.watchForChange) { + ClientDoc docio = client.watch(0); + if (docio!=null) { client.disableGui(true); Cache.log.debug("Updating jalview from changed vamsas document."); - client.updateJalview(docio); + client.updateJalview(docio); Cache.log.debug("Finished updating from document change."); docio.closeDoc(); docio=null; client.disableGui(false); - } + } } running=false; - } + } - } + } public void disableGui(boolean b) { - Desktop.instance.setVamsasUpdate(b); + Desktop.instance.setVamsasUpdate(b); } public void startWatcher() { if (watcher==null) -- 1.7.10.2