From e5c2e37b24f09c90f2f7c748f6be10ce025da261 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 13 Sep 2005 17:44:08 +0000
Subject: [PATCH] Warn if out of memory

---
 src/jalview/gui/PCAPanel.java   |   94 ++++++++++++++++++++++-----------------
 src/jalview/ws/JPredClient.java |   12 +++++
 src/jalview/ws/MsaWSClient.java |   24 +++++++---
 3 files changed, 85 insertions(+), 45 deletions(-)

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 474a158..d1005c2 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -28,6 +28,7 @@ import java.awt.*;
 import java.awt.event.*;
 
 import java.util.*;
+import javax.swing.JOptionPane;
 
 
 /**
@@ -89,46 +90,59 @@ public class PCAPanel extends GPCAPanel implements Runnable
      */
     public void run()
     {
-                pca = new PCA(seqs);
-                pca.run();
-
-                // Now find the component coordinates
-                int ii = 0;
-
-                while ((ii < seqs.length) && (seqs[ii] != null))
-                {
-                    ii++;
-                }
-
-                double[][] comps = new double[ii][ii];
-
-                for (int i = 0; i < ii; i++)
-                {
-                    if (pca.getEigenvalue(i) > 1e-4)
-                    {
-                        comps[i] = pca.component(i);
-                    }
-                }
-
-                //////////////////
-                xCombobox.setSelectedIndex(0);
-                yCombobox.setSelectedIndex(1);
-                zCombobox.setSelectedIndex(2);
-
-                top = pca.getM().rows - 1;
-
-                Vector points = new Vector();
-                float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
-
-                for (int i = 0; i < pca.getM().rows; i++)
-                {
-                    SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
-                    points.addElement(sp);
-                }
-
-                rc.setPoints(points, pca.getM().rows);
-                rc.repaint();
-                seqs = null;
+      try{
+        pca = new PCA(seqs);
+        pca.run();
+
+        // Now find the component coordinates
+        int ii = 0;
+
+        while ( (ii < seqs.length) && (seqs[ii] != null))
+        {
+          ii++;
+        }
+
+        double[][] comps = new double[ii][ii];
+
+        for (int i = 0; i < ii; i++)
+        {
+          if (pca.getEigenvalue(i) > 1e-4)
+          {
+            comps[i] = pca.component(i);
+          }
+        }
+
+        //////////////////
+        xCombobox.setSelectedIndex(0);
+        yCombobox.setSelectedIndex(1);
+        zCombobox.setSelectedIndex(2);
+
+        top = pca.getM().rows - 1;
+
+        Vector points = new Vector();
+        float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+        for (int i = 0; i < pca.getM().rows; i++)
+        {
+          SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+          points.addElement(sp);
+        }
+
+        rc.setPoints(points, pca.getM().rows);
+        rc.repaint();
+        seqs = null;
+      }
+     catch(OutOfMemoryError er)
+      { JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "Out of memory calculating PCA!!"
+                                              +
+                                              "\nSee help files for increasing Java Virtual Machine memory."
+                                              , "Out of memory",
+                                              JOptionPane.WARNING_MESSAGE);
+        System.out.println("PCAPanel: "+er);
+
+      }
+
     }
 
     /**
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 4302df2..80a66c3 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -248,6 +248,18 @@ public class JPredClient
           {
           }
         }
+        catch (OutOfMemoryError er)
+        {
+          jobComplete = true;
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Out of memory handling result!!"
+                                                +
+              "\nSee help files for increasing Java Virtual Machine memory."
+                                                , "Out of memory",
+                                                JOptionPane.WARNING_MESSAGE);
+          System.out.println("JPredClient: "+er);
+        }
       }
       if (result!=null)
         if (! (result.isJobFailed() || result.isServerError()))
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 7f754e0..0d4b2c1 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -280,8 +280,9 @@ public class MsaWSClient
           {
             if (result.getStatus() != null)
             {
-              wsInfo.setProgressText(OutputHeader + "\n" +
-                                     result.getStatus());
+              System.out.println("result "+result.getStatus().length());
+              wsInfo.setProgressText(OutputHeader + "\n" );
+                                //     result.getStatus());
             }
             if (result.isServerError())
             {
@@ -325,6 +326,16 @@ public class MsaWSClient
           {
           }
         }
+        catch(OutOfMemoryError er)
+        {
+          jobComplete = true;
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Out of memory handling result!!"
+             +"\nSee help files for increasing Java Virtual Machine memory."
+             ,"Out of memory", JOptionPane.WARNING_MESSAGE );
+          System.out.println("MsaWSClient: "+er);
+        }
       }
 
       if (allowedServerExceptions == 0)
@@ -425,18 +436,21 @@ public class MsaWSClient
 
         if (result.getStatus() != null)
         {
-          OutputHeader += ("\n" + result.getStatus());
+          System.out.println("get status  " +result.getStatus().length());
+         // OutputHeader += ("\n" + result.getStatus());
         }
 
         if (result.getMsa() != null)
         {
-          OutputHeader += "\nAlignment Object Method Notes\n";
+          System.out.println("get msa");
+       //   OutputHeader += "\nAlignment Object Method Notes\n";
 
           String[] lines = result.getMsa().getMethod();
 
+System.out.println("lines "+lines.length);
           for (int line = 0; line < lines.length; line++)
           {
-            OutputHeader += (lines[line] + "\n");
+           // OutputHeader += (lines[line] + "\n");
           }
 
           // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
-- 
1.7.10.2