From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 8 Jul 2011 14:59:02 +0000 (+0100)
Subject: open each query result from an alignment datasource as a
X-Git-Tag: Release_2_7~142
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=56d8f0b05df600ea54388d58cf505d911beb630a;p=jalview.git

open each query result from an alignment datasource as a
different alignment (JAL-865)
---

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index b9442df..e060b54 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -125,4 +125,9 @@ public class DBRefSource
    * time.
    */
   public static final Object MULTIACC = "MULTIACC";
+
+  /**
+   * DB query returns an alignment for each accession provided.
+   */
+  public static final Object ALIGNMENTDB = "ALIGNMENTS";
 }
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index b7cccf7..14c0a00 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -444,9 +444,11 @@ public class SequenceFetcher extends JPanel implements Runnable
       resetDialog();
       return;
     }
-    AlignmentI aresult = null;
+    ArrayList<String> aresultq=new ArrayList<String>();
+    ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
     Object source = database.getSelectedItem();
     Enumeration en = new StringTokenizer(textArea.getText(), ";");
+    boolean isAliSource=false;
     try
     {
       guiWindow.setProgressBar(
@@ -454,6 +456,7 @@ public class SequenceFetcher extends JPanel implements Runnable
               Thread.currentThread().hashCode());
       DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
               .get(source));
+      isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
       if (proxy.getAccessionSeparator() == null)
       {
         while (en.hasMoreElements())
@@ -485,14 +488,8 @@ public class SequenceFetcher extends JPanel implements Runnable
             }
             if (indres != null)
             {
-              if (aresult == null)
-              {
-                aresult = indres;
-              }
-              else
-              {
-                aresult.append(indres);
-              }
+              aresultq.add(item);
+              aresult.add(indres);
             }
           } catch (Exception e)
           {
@@ -514,7 +511,8 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         try
         {
-          aresult = proxy.getSequenceRecords(multiacc.toString());
+          aresultq.add(multiacc.toString());
+          aresult.add(proxy.getSequenceRecords(multiacc.toString()));
         } catch (OutOfMemoryError oome)
         {
           new OOMWarning("fetching " + multiacc + " from "
@@ -547,9 +545,24 @@ public class SequenceFetcher extends JPanel implements Runnable
               + " from " + database.getSelectedItem());
       e.printStackTrace();
     }
-    if (aresult != null)
+    if (aresult != null && aresult.size()>0)
     {
-      parseResult(aresult, null, null);
+      AlignmentI ar=null;
+      if (isAliSource) {
+        // new window for each result
+        while (aresult.size()>0)
+        {
+          parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
+        }
+      } else {
+        // concatenate all results in one window
+        while (aresult.size()>0)
+        {
+          if (ar==null) { ar = aresult.remove(0);}
+          else { ar.append(aresult.remove(0)); };
+        }
+        parseResult(ar, null, null);
+      } 
     }
     // only remove visual delay after we finished parsing.
     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
@@ -728,6 +741,13 @@ public class SequenceFetcher extends JPanel implements Runnable
     return null;
   }
 
+  /**
+   * 
+   * @return a standard title for any results retrieved using the currently selected source and settings
+   */
+  public String getDefaultRetrievalTitle() {
+    return "Retrieved from " + database.getSelectedItem();
+  }
   AlignmentI parseResult(AlignmentI al, String title,
           String currentFileFormat)
   {
@@ -748,7 +768,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         if (title == null)
         {
-          title = "Retrieved from " + database.getSelectedItem();
+          title = getDefaultRetrievalTitle();
         }
         SequenceFeature[] sfs = null;
         for (Enumeration sq = al.getSequences().elements(); sq
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 834dd12..1b2a0c4 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -46,6 +46,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
     super();
     // all extensions of this PFAM source base class are DOMAINDB sources
     addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
+    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
   }
 
   /*
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index 9c5356a..67097ef 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -120,4 +120,12 @@ public interface DbSourceProxy
    * @return one or more string buffers for each individual query
    */
   public StringBuffer getRawRecords();
+
+  
+  /**
+   * Find out more info about the source.
+   * @param dbsourceproperty - one of the database reference source properties in jalview.datamodel.DBRefSource
+   * @return true if the source has this property
+   */
+  public boolean isA(Object dbsourceproperty);
 }
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index 44de157..94d7577 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -128,4 +128,12 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
     return sequences;
   }
 
+  @Override
+  public boolean isA(Object dbsourceproperty)
+  {
+    assert(dbsourceproperty!=null);
+    return (props==null) ? false : props.containsKey(dbsourceproperty);
+  }
+  
+
 }