From 4edc470836068d06d8033a849f7eec780d39eb99 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
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