X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=b20ebbb5f2d611b1a6d20f3e31fcc958cd525d13;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=0d93cb82902834cbec7e09fbc49efd48235ff556;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 0d93cb8..b20ebbb 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
 import java.util.ArrayList;
@@ -19,7 +37,8 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 /**
  * This is the the concrete implementation of the sequence retrieval interface
  * and abstract class in jalview.ws.seqfetcher. This implements the run-time
- * discovery of sequence database clients, and provides a hardwired main for testing all registered handlers. 
+ * discovery of sequence database clients, and provides a hardwired main for
+ * testing all registered handlers.
  * 
  */
 public class SequenceFetcher extends ASequenceFetcher
@@ -38,17 +57,22 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
     addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed alignment is 'default' for PFAM
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
+                                                              // alignment is
+                                                              // 'default' for
+                                                              // PFAM
     registerDasSequenceSources();
   }
+
   /**
-   * return an ordered list of database sources suitable for using in a GUI element
+   * return an ordered list of database sources suitable for using in a GUI
+   * element
    */
-  public String[] getOrderedSupportedSources() {
+  public String[] getOrderedSupportedSources()
+  {
     String[] srcs = this.getSupportedDb();
-    ArrayList dassrc = new ArrayList(),
-      nondas=new ArrayList();
-    for (int i=0;i<srcs.length;i++)
+    ArrayList dassrc = new ArrayList(), nondas = new ArrayList();
+    for (int i = 0; i < srcs.length; i++)
     {
       String nm = getSourceProxy(srcs[i]).getDbName();
       if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.DasSequenceSource)
@@ -57,21 +81,25 @@ public class SequenceFetcher extends ASequenceFetcher
         {
           nm = nm.substring(4);
         }
-        dassrc.add(new String[] { srcs[i], nm.toUpperCase()} );
-      } else {
-        nondas.add(new String[] { srcs[i], nm.toUpperCase()} );
+        dassrc.add(new String[]
+        { srcs[i], nm.toUpperCase() });
+      }
+      else
+      {
+        nondas.add(new String[]
+        { srcs[i], nm.toUpperCase() });
       }
     }
     Object[] sorted = nondas.toArray();
     String[] tosort = new String[sorted.length];
     nondas.clear();
-    for (int j=0;j<sorted.length;j++)
+    for (int j = 0; j < sorted.length; j++)
     {
       tosort[j] = ((String[]) sorted[j])[1];
     }
     jalview.util.QuickSort.sort(tosort, sorted);
-    int i=0;
-    for (int j=sorted.length-1;j>=0; j--,i++)
+    int i = 0;
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
     {
       srcs[i] = ((String[]) sorted[j])[0];
       sorted[j] = null;
@@ -80,20 +108,22 @@ public class SequenceFetcher extends ASequenceFetcher
     sorted = dassrc.toArray();
     tosort = new String[sorted.length];
     dassrc.clear();
-    for (int j=0;j<sorted.length;j++)
+    for (int j = 0; j < sorted.length; j++)
     {
       tosort[j] = ((String[]) sorted[j])[1];
     }
     jalview.util.QuickSort.sort(tosort, sorted);
-    for (int j=sorted.length-1;j>=0; j--,i++)
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
     {
       srcs[i] = ((String[]) sorted[j])[0];
       sorted[j] = null;
     }
     return srcs;
   }
+
   /**
    * simple run method to test dbsources.
+   * 
    * @param argv
    */
   public static void main(String[] argv)
@@ -101,12 +131,12 @@ public class SequenceFetcher extends ASequenceFetcher
     AlignmentI ds = null;
     Vector noProds = new Vector();
     String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"
-      +"With no arguments, all DbSources will be queried with their test Accession number.\n"
-      +"If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
+            + "With no arguments, all DbSources will be queried with their test Accession number.\n"
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
     if (argv != null && argv.length > 0)
     {
       DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);
-      if (sp!=null)
+      if (sp != null)
       {
         AlignmentI al = null;
         try
@@ -115,40 +145,46 @@ public class SequenceFetcher extends ASequenceFetcher
         } catch (Exception e)
         {
           e.printStackTrace();
-          System.err.println("Error when retrieving "+argv[1]+" from "+argv[0]+"\nUsage: "+usage);
+          System.err.println("Error when retrieving " + argv[1] + " from "
+                  + argv[0] + "\nUsage: " + usage);
         }
         SequenceI[] prod = al.getSequencesArray();
-        if (al!=null)
+        if (al != null)
         {
           for (int p = 0; p < prod.length; p++)
           {
             System.out.println("Prod " + p + ": "
-                    + prod[p].getDisplayId(true) + " : "+prod[p].getDescription());
+                    + prod[p].getDisplayId(true) + " : "
+                    + prod[p].getDescription());
           }
         }
         return;
-      } else {
-        System.err.println("Can't resolve "+argv[0]+" as a database name. Allowed values are :\n"+new SequenceFetcher().getSupportedDb());
       }
-      System.out
-              .println(usage);
+      else
+      {
+        System.err.println("Can't resolve " + argv[0]
+                + " as a database name. Allowed values are :\n"
+                + new SequenceFetcher().getSupportedDb());
+      }
+      System.out.println(usage);
     }
     ASequenceFetcher sfetcher = new SequenceFetcher();
     String[] dbSources = sfetcher.getSupportedDb();
-    for (int dbsource=0; dbsource<dbSources.length;dbsource++)
+    for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
     {
       String db = dbSources[dbsource];
       // skip me
       if (db.equals(DBRefSource.PDB))
         continue;
       DbSourceProxy sp = sfetcher.getSourceProxy(db);
-      System.out
-              .println("Source: "+sp.getDbName()+" (" + db + "): retrieving test:" + sp.getTestQuery());
+      System.out.println("Source: " + sp.getDbName() + " (" + db
+              + "): retrieving test:" + sp.getTestQuery());
       AlignmentI al = null;
       try
       {
         al = sp.getSequenceRecords(sp.getTestQuery());
-        if (al != null && al.getHeight() > 0 && sp.getDbSourceProperties()!=null)
+        if (al != null && al.getHeight() > 0
+                && sp.getDbSourceProperties() != null)
         {
           boolean dna = sp.getDbSourceProperties().containsKey(
                   DBRefSource.DNACODINGSEQDB)
@@ -248,7 +284,8 @@ public class SequenceFetcher extends ASequenceFetcher
         Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
                 seqs, dna, null, ds);
         System.out.println("Found "
-                + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");
+                + ((prodal == null) ? "no" : "" + prodal.getHeight())
+                + " products");
         if (prodal != null)
         {
           SequenceI[] prod = prodal.getSequencesArray(); // note
@@ -262,7 +299,7 @@ public class SequenceFetcher extends ASequenceFetcher
           // mapping
           // (if
           // present)
-            for (int p = 0; p < prod.length; p++)
+          for (int p = 0; p < prod.length; p++)
           {
             System.out.println("Prod " + p + ": "
                     + prod[p].getDisplayId(true));
@@ -272,53 +309,67 @@ public class SequenceFetcher extends ASequenceFetcher
 
     }
   }
+
   /**
-   * query the currently defined DAS source registry for sequence sources and add a DasSequenceSource instance for each source to the SequenceFetcher source list.
+   * query the currently defined DAS source registry for sequence sources and
+   * add a DasSequenceSource instance for each source to the SequenceFetcher
+   * source list.
    */
-  public void registerDasSequenceSources() {
-    DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();
-    for (int s=0;s<sources.length; s++)
+  public void registerDasSequenceSources()
+  {
+    DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher
+            .getDASSources();
+    for (int s = 0; s < sources.length; s++)
     {
-      Das1Source d1s=null;
+      Das1Source d1s = null;
       if (sources[s].hasCapability("sequence"))
       {
         if (sources[s] instanceof Das2Source)
         {
-          if (((Das2Source)sources[s]).hasDas1Capabilities()) {
-            try {
-              d1s = org.biojava.dasobert.das2.DasSourceConverter.toDas1Source((Das2Source) sources[s]);
+          if (((Das2Source) sources[s]).hasDas1Capabilities())
+          {
+            try
+            {
+              d1s = org.biojava.dasobert.das2.DasSourceConverter
+                      .toDas1Source((Das2Source) sources[s]);
             } catch (Exception e)
             {
-              System.err.println("Ignoring DAS2 sequence source "+sources[s].getNickname()+" - couldn't map to Das1Source.\n");
+              System.err.println("Ignoring DAS2 sequence source "
+                      + sources[s].getNickname()
+                      + " - couldn't map to Das1Source.\n");
               e.printStackTrace();
             }
           }
-        } else {
+        }
+        else
+        {
           if (sources[s] instanceof Das1Source)
-          { 
+          {
             d1s = (Das1Source) sources[s];
           }
         }
       }
-      if (d1s!=null)
+      if (d1s != null)
       {
         DasCoordinateSystem[] css = d1s.getCoordinateSystem();
-        for (int c=0;c<css.length;c++)
+        for (int c = 0; c < css.length; c++)
         {
-          try {
-            addDbRefSourceImpl(
-                    new jalview.ws.dbsources.DasSequenceSource("das:"+d1s.getNickname()+" ("+css[c].getName()+")",
-                            css[c].getName(),d1s, css[c]));
+          try
+          {
+            addDbRefSourceImpl(new jalview.ws.dbsources.DasSequenceSource(
+                    "das:" + d1s.getNickname() + " (" + css[c].getName()
+                            + ")", css[c].getName(), d1s, css[c]));
           } catch (Exception e)
           {
-            System.err.println("Ignoring sequence coord system "+c+" ("+
-                    css[c].getName()+") for source "+d1s.getNickname()
+            System.err.println("Ignoring sequence coord system " + c + " ("
+                    + css[c].getName() + ") for source "
+                    + d1s.getNickname()
                     + "- threw exception when constructing fetcher.\n");
             e.printStackTrace();
           }
         }
       }
-          
+
     }
   }