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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui ApolloFrame.java,1.140,1.141 Config.java,1.116,1.117 Controller.java,1.36,1.37 DataLoader.java,1.36,1.37
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From: Suzanna L. <su...@us...> - 2003-04-30 01:53:38
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Update of /cvsroot/gmod/apollo/src/java/apollo/gui
In directory sc8-pr-cvs1:/tmp/cvs-serv31356/apollo/gui
Modified Files:
ApolloFrame.java Config.java Controller.java DataLoader.java
Log Message:
after much diligent exertion found bug in splitting of tandem
repeats.
also saving history of GUI input correctly now
Index: ApolloFrame.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/ApolloFrame.java,v
retrieving revision 1.140
retrieving revision 1.141
diff -C2 -d -r1.140 -r1.141
*** ApolloFrame.java 22 Apr 2003 22:50:49 -0000 1.140
--- ApolloFrame.java 30 Apr 2003 01:53:28 -0000 1.141
***************
*** 683,694 ****
if (options[0].equals(result)){
okay = true;
! // This seems to happen when user made some changes, tried to load another dataset,
! // the load failed, and now we've asked again "Save your changes?" and the user
! // said no but we can't get the adapter.
! // LoadUtil was setting adapter to null on failed loads - doesnt do this
! // anymore - DataLoader only sets adapter if it gets a valid one - MG
! //if (getAdapter() == null) { return true; }
! //Annotations are willfully discarded. However, the user
! //may still have outstanding locks. We message the adapter to roll the locks back.
rollbackResult = getAdapter().rollbackAnnotations(getCurationSet());
if(rollbackResult = false){
--- 683,697 ----
if (options[0].equals(result)){
okay = true;
! // This seems to happen when user made some changes,
! // tried to load another dataset,
! // the load failed, and now we've asked again "Save your changes?"
! // and the user said no but we can't get the adapter.
! // LoadUtil was setting adapter to null on failed loads -
! // doesnt do this anymore - DataLoader only sets adapter
! // if it gets a valid one - MG
! // if (getAdapter() == null) { return true; }
! // Annotations are willfully discarded. However, the user
! // may still have outstanding locks. We message the adapter
! // to roll the locks back.
rollbackResult = getAdapter().rollbackAnnotations(getCurationSet());
if(rollbackResult = false){
***************
*** 703,708 ****
}else{
//
! //No annotations were made - so movement should be possible. However, the user
! //may still have outstanding locks. We message the adapter to roll the locks back.
if (getAdapter() != null) {
rollbackResult = getAdapter().rollbackAnnotations(getCurationSet());
--- 706,712 ----
}else{
//
! // No annotations were made - so movement should be possible.
! // However, the user may still have outstanding locks.
! // We message the adapter to roll the locks back.
if (getAdapter() != null) {
rollbackResult = getAdapter().rollbackAnnotations(getCurationSet());
Index: Config.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/Config.java,v
retrieving revision 1.116
retrieving revision 1.117
diff -C2 -d -r1.116 -r1.117
*** Config.java 25 Apr 2003 18:17:45 -0000 1.116
--- Config.java 30 Apr 2003 01:53:29 -0000 1.117
***************
*** 115,119 ****
static void setDataAdapterType(String adapterType) {
if (!adapterToStyle.containsKey(adapterType)) {
! System.out.println("Failed to set style "+adapterType+"--couldn't find style file");
return; //??
}
--- 115,120 ----
static void setDataAdapterType(String adapterType) {
if (!adapterToStyle.containsKey(adapterType)) {
! System.out.println("Failed to set style "+adapterType+
! "--couldn't find style file");
return; //??
}
***************
*** 126,131 ****
static void setStyle(Style s) {
! // second parameter is whether to update the style hashtable with this new style
! setStyle(s, false);
}
--- 127,133 ----
static void setStyle(Style s) {
! // second parameter is whether to update
! // the style hashtable with this new style
! setStyle(s, false);
}
***************
*** 137,142 ****
if (updateStyleHash) {
filenameToStyle.put(styleFile, s);
! // Now we have to go through the hashtable and find all the keys whose value
! // is this style...
Iterator keys = adapterToStyle.keySet().iterator();
while (keys.hasNext()) {
--- 139,144 ----
if (updateStyleHash) {
filenameToStyle.put(styleFile, s);
! // Now we have to go through the hashtable and find all
! // the keys whose value is this style...
Iterator keys = adapterToStyle.keySet().iterator();
while (keys.hasNext()) {
***************
*** 151,156 ****
/** Data adapter has changed - fetch the matching style */
public static void newDataAdapter(DataAdapter da) {
! setDataAdapterType(da.getClass().getName()); // Sets global variable "style"
! System.out.println("Set style to " + da.getClass().getName() + "; style file is " + style.getFileName());
}
--- 153,160 ----
/** Data adapter has changed - fetch the matching style */
public static void newDataAdapter(DataAdapter da) {
! // Sets global variable "style"
! setDataAdapterType(da.getClass().getName());
! /* System.out.println("Set style to " + da.getClass().getName() +
! "; style file is " + style.getFileName()); */
}
***************
*** 623,627 ****
} else if (key.equalsIgnoreCase("DataAdapterInstall")) {
// a mandatory data adapter style is in value2
- // System.out.println("Data adapter install: "+value);
installDataAdapter(value,value2);
setDataAdapterType(value);
--- 627,630 ----
***************
*** 854,858 ****
// set them now.
setDefaultHistoryAndAutosaveLocs();
- // System.out.println("Successfuly initialized");
}
}
--- 857,860 ----
Index: Controller.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/Controller.java,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** Controller.java 7 Mar 2003 16:09:06 -0000 1.36
--- Controller.java 30 Apr 2003 01:53:29 -0000 1.37
***************
*** 28,31 ****
--- 28,34 ----
Hashtable windowHash = new Hashtable();
boolean annotations_changed = false;
+ // SUZ This is to indicate whether this is a first time ever
+ // or a curation set has previously been loaded
+ boolean curation_loaded = false;
public Controller() {
***************
*** 115,120 ****
--- 118,134 ----
}
+ public boolean isCurationSetLoaded () {
+ return curation_loaded;
+ }
+
public void setAnnotationChanged (boolean un_saved) {
annotations_changed = un_saved;
+ }
+
+ public void curationSetIsLoaded (boolean loaded) {
+ // never let this be set to false, once anything has
+ // loaded then this is true
+ if (loaded)
+ curation_loaded = loaded;
}
Index: DataLoader.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/DataLoader.java,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** DataLoader.java 19 Feb 2003 23:40:41 -0000 1.36
--- DataLoader.java 30 Apr 2003 01:53:31 -0000 1.37
***************
*** 40,49 ****
Properties props,
ProgressListener listener)
! throws apollo.dataadapter.DataAdapterException {
try {
DataAdapterRegistry
! adapterRegistry
! = Config.getAdapterRegistry
! ();
ApolloDataAdapterI datasource = (ApolloDataAdapterI)
adapterRegistry.getAdapter(props.getProperty("adapter"));
--- 40,47 ----
Properties props,
ProgressListener listener)
! throws apollo.dataadapter.DataAdapterException {
try {
DataAdapterRegistry
! adapterRegistry = Config.getAdapterRegistry();
ApolloDataAdapterI datasource = (ApolloDataAdapterI)
adapterRegistry.getAdapter(props.getProperty("adapter"));
***************
*** 56,60 ****
System.out.println(" "+names[i]);
}
! } else {
// clean up old curation set (remove as listener)
if (curation_set!=null)
--- 54,59 ----
System.out.println(" "+names[i]);
}
! }
! else {
// clean up old curation set (remove as listener)
if (curation_set!=null)
***************
*** 65,69 ****
curation_set = getData(frame, datasource, listener);
}
! } catch (Exception ie) {
throw new apollo.dataadapter.DataAdapterException(ie.getMessage(), ie);
}
--- 64,69 ----
curation_set = getData(frame, datasource, listener);
}
! }
! catch (Exception ie) {
throw new apollo.dataadapter.DataAdapterException(ie.getMessage(), ie);
}
***************
*** 99,105 ****
if (args.length >= 2) {
DataAdapterRegistry
! adapterRegistry
! = Config.getAdapterRegistry
! ();
try {
if (args[0].equals("-f") || args[0].equals("-g")) {
--- 99,103 ----
if (args.length >= 2) {
DataAdapterRegistry
! adapterRegistry = Config.getAdapterRegistry();
try {
if (args[0].equals("-f") || args[0].equals("-g")) {
***************
*** 187,247 ****
// were being thrown on Alphas.
Runnable chooserRun = new Runnable() {
! public void run() {
! ApolloAdapterChooser chooser
! // Adding ApolloFrame first arg in an attempt to keep this window always on top
! = new ApolloAdapterChooser((ApolloFrame)frame,
! Config.getAdapterRegistry(),
! ApolloDataAdapterI.OP_READ_DATA,
! "Apollo: load data",
! null,
! true); // last arg is "failfast"
! chooser.setBackground(Config.getDataLoaderBackgroundColor());
! chooser.setForeground(Config.getDataLoaderLabelColor());
!
! String historyFile = Config.getAdapterHistoryFile();
! if (historyFile != null && historyFile.length() > 0)
! chooser.setPropertiesFile(new File(historyFile));
! chooser.show();
! chooser.invalidate();
! // DataAdapterChooser ignores setLocation, for some reason
! // chooser.setLocation(100,10);
! chooser.validate();
! if (!chooser.isCancelled() && !chooser.isFailure()) {
! DataAdapter adapter = chooser.getDataAdapter();
! if (adapter instanceof ApolloDataAdapterI) {
! data_adapter = (ApolloDataAdapterI) adapter;
! Config.setDataAdapterType(data_adapter.getClass().getName());
! // frame can be null on first load
! //frame.setAdapter(data_adapter);
! }
! return_value = (CurationSet) chooser.getOutput();
! } else if (chooser.isFailure()) {
! org.bdgp.io.DataAdapterException ex = chooser.getException();
! String message = ex.getMessage();
! JOptionPane msg = new JOptionPane();
! JFrame parent = (frame instanceof JFrame ?
! (JFrame) frame : null);
! msg.showMessageDialog(parent,
! message,
! "Read error",
! JOptionPane.WARNING_MESSAGE);
! return_value = null;
! } else if (chooser.isCancelled()) {
! if (quitOnCancel) {
! System.out.println ("Nothing loaded so quitting");
! System.exit(0);
! }
! return_value = null;
! }
! // This dispose is critical. Without it the DataAdapterChooser
! // lingers as its a top level window(JDialog) and it keeps
! // a reference to the curation set - major mem leak.
! chooser.dispose();
! chooser = null;
! }
! }
! ; // end of Runnable
chooserRun.run();
if (return_value == null)
--- 185,245 ----
// were being thrown on Alphas.
Runnable chooserRun = new Runnable() {
! public void run() {
! ApolloAdapterChooser chooser
! // Adding ApolloFrame first arg in an attempt
! // to keep this window always on top
! = new ApolloAdapterChooser((ApolloFrame)frame,
! Config.getAdapterRegistry(),
! ApolloDataAdapterI.OP_READ_DATA,
! "Apollo: load data",
! null,
! // last arg is "failfast"
! true);
! chooser.setBackground(Config.getDataLoaderBackgroundColor());
! chooser.setForeground(Config.getDataLoaderLabelColor());
! String historyFile = Config.getAdapterHistoryFile();
! if (historyFile != null && historyFile.length() > 0)
! chooser.setPropertiesFile(new File(historyFile));
! chooser.show();
! chooser.invalidate();
! // DataAdapterChooser ignores setLocation, for some reason
! // chooser.setLocation(100,10);
! chooser.validate();
! if (!chooser.isCancelled() && !chooser.isFailure()) {
! DataAdapter adapter = chooser.getDataAdapter();
! if (adapter instanceof ApolloDataAdapterI) {
! data_adapter = (ApolloDataAdapterI) adapter;
! Config.setDataAdapterType(data_adapter.getClass().getName());
! }
! return_value = (CurationSet) chooser.getOutput();
! }
! else if (chooser.isFailure()) {
! org.bdgp.io.DataAdapterException ex = chooser.getException();
! String message = ex.getMessage();
! JOptionPane msg = new JOptionPane();
! JFrame parent = (frame instanceof JFrame ?
! (JFrame) frame : null);
! msg.showMessageDialog(parent,
! message,
! "Read error",
! JOptionPane.WARNING_MESSAGE);
! return_value = null;
! } else if (chooser.isCancelled()) {
! if (quitOnCancel) {
! System.out.println ("Nothing loaded so quitting");
! System.exit(0);
! }
! return_value = null;
! }
+ // This dispose is critical. Without it the DataAdapterChooser
+ // lingers as its a top level window(JDialog) and it keeps
+ // a reference to the curation set - major mem leak.
+ chooser.dispose();
+ chooser = null;
+ }
+ }
+ ; // end of Runnable
chooserRun.run();
if (return_value == null)
***************
*** 253,257 ****
// Do gc here to stop initial pause on first scroll
System.gc();
! } else { // datasource is nonnull
data_adapter = datasource;
Config.setDataAdapterType(data_adapter.getClass().getName());
--- 251,256 ----
// Do gc here to stop initial pause on first scroll
System.gc();
! }
! else { // datasource is nonnull
data_adapter = datasource;
Config.setDataAdapterType(data_adapter.getClass().getName());
***************
*** 264,268 ****
try {
out = datasource.getCurationSet();
! } catch (apollo.dataadapter.DataAdapterException e) {
JOptionPane msg = new JOptionPane();
JFrame parent = (frame instanceof JFrame ?
--- 263,268 ----
try {
out = datasource.getCurationSet();
! }
! catch (apollo.dataadapter.DataAdapterException e) {
JOptionPane msg = new JOptionPane();
JFrame parent = (frame instanceof JFrame ?
***************
*** 279,282 ****
--- 279,283 ----
// System.out.println("Data read time = " +
// (curtime - lasttime) + "ms.");
+ Config.getController().curationSetIsLoaded (out != null);
return out;
}
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