From eb07e696db878b45a4738f95e58eaef347d719c3 Mon Sep 17 00:00:00 2001
From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 21 May 2012 03:17:52 +0000
Subject: [PATCH] in progress

---
 .../archaeopteryx/tools/PhylogeneticInferrer.java  |   22 ++++++++++----------
 .../forester/archaeopteryx/tools/ProcessPool.java  |   10 ++++++++-
 2 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 7e0ec77..4f17c69 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -64,7 +64,7 @@ public class PhylogeneticInferrer implements Runnable {
     private final MainFrameApplication         _mf;
     private final PhylogeneticInferenceOptions _options;
     private final List<Sequence>               _seqs;
-    private final boolean DEBUG = true;
+    private final boolean                      DEBUG           = true;
     public final static String                 MSA_FILE_SUFFIX = ".aln";
     public final static String                 PWD_FILE_SUFFIX = ".pwd";
 
@@ -89,9 +89,9 @@ public class PhylogeneticInferrer implements Runnable {
     private Msa inferMsa() throws IOException, InterruptedException {
         final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
         if ( DEBUG ) {
-        System.out.println();
-        System.out.println( "temp file: " + temp_seqs_file );
-        System.out.println();
+            System.out.println();
+            System.out.println( "temp file: " + temp_seqs_file );
+            System.out.println();
         }
         //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
         final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
@@ -170,7 +170,7 @@ public class PhylogeneticInferrer implements Runnable {
                                                "Failed to Calculate MSA",
                                                JOptionPane.ERROR_MESSAGE );
                 if ( DEBUG ) {
-                e.printStackTrace();
+                    e.printStackTrace();
                 }
                 return;
             }
@@ -183,7 +183,7 @@ public class PhylogeneticInferrer implements Runnable {
                                                "Unexpected Exception During MSA Calculation",
                                                JOptionPane.ERROR_MESSAGE );
                 if ( DEBUG ) {
-                e.printStackTrace();
+                    e.printStackTrace();
                 }
                 return;
             }
@@ -197,8 +197,8 @@ public class PhylogeneticInferrer implements Runnable {
                 return;
             }
             if ( DEBUG ) {
-            System.out.println( msa.toString() );
-            System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
+                System.out.println( msa.toString() );
+                System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
             }
             final MsaMethods msa_tools = MsaMethods.createInstance();
             if ( _options.isExecuteMsaProcessing() ) {
@@ -216,9 +216,9 @@ public class PhylogeneticInferrer implements Runnable {
                 }
             }
             if ( DEBUG ) {
-            System.out.println( msa_tools.getIgnoredSequenceIds() );
-            System.out.println( msa.toString() );
-            System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
+                System.out.println( msa_tools.getIgnoredSequenceIds() );
+                System.out.println( msa.toString() );
+                System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
             }
             _msa = msa;
         }
diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java b/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java
index 0c4ed99..0e58ca2 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java
@@ -30,6 +30,7 @@ import java.util.List;
 
 public class ProcessPool {
 
+    private final static boolean                   DEBUG      = true;
     final static private ArrayList<ProcessRunning> _processes = new ArrayList<ProcessRunning>();
 
     public synchronized ProcessRunning getProcessByIndex( final int i ) {
@@ -53,15 +54,22 @@ public class ProcessPool {
         final ProcessRunning p = ProcessRunning.createInstance( name );
         final int id = p.getId();
         if ( getProcessById( id ) != null ) {
-            throw new IllegalStateException( "process with id " + id + "already exists" );
+            throw new IllegalStateException( " process with id " + id + "already exists" );
         }
         getProcesses().add( p );
+        if ( DEBUG ) {
+            System.out.println( "added: " + p );
+        }
         return id;
     }
 
     public synchronized boolean removeProcess( final int id ) {
         final int i = getProcessIndexById( id );
         if ( i >= 0 ) {
+            if ( DEBUG ) {
+                final ProcessRunning p = getProcessById( id );
+                System.out.println( " removing: " + p );
+            }
             getProcesses().remove( i );
             return true;
         }
-- 
1.7.10.2