JAL-1925 update source version in license

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 416773d..182f2f4 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,8 @@
  */
 package jalview.io;
 
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -37,12 +38,50 @@ import jalview.datamodel.SequenceI;
  */
 public class FormatAdapter extends AppletFormatAdapter
 {
+  public FormatAdapter(AlignmentViewPanel viewpanel)
+  {
+    super(viewpanel);
+    init();
+  }
+
+  public FormatAdapter()
+  {
+    super();
+    init();
+  }
+
+  public FormatAdapter(AlignmentViewPanel alignPanel,
+          AlignExportSettingI settings)
+  {
+    super(alignPanel, settings);
+  }
+
+  private void init()
+  {
+    if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+    {
+      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+              true);
+      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+              true);
+      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+              true);
+    }
+    else
+    {
+      // disable all PDB annotation options
+      annotFromStructure = false;
+      localSecondaryStruct = false;
+      serviceSecondaryStruct = false;
+    }
+  }
 
   public String formatSequences(String format, SequenceI[] seqs,
-          String[] omitHiddenColumns)
+          String[] omitHiddenColumns, int[] exportRange)
   {
 
-    return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+    return formatSequences(format,
+            replaceStrings(seqs, omitHiddenColumns, exportRange));
   }
 
   /**
@@ -54,15 +93,44 @@ public class FormatAdapter extends AppletFormatAdapter
    * @return new sequences
    */
   public SequenceI[] replaceStrings(SequenceI[] seqs,
-          String[] omitHiddenColumns)
+          String[] omitHiddenColumns, int[] startEnd)
   {
     if (omitHiddenColumns != null)
     {
       SequenceI[] tmp = new SequenceI[seqs.length];
+
+      int startRes;
+      int endRes;
+      int startIndex;
+      int endIndex;
       for (int i = 0; i < seqs.length; i++)
       {
+        startRes = seqs[i].getStart();
+        endRes = seqs[i].getEnd();
+        if (startEnd != null)
+        {
+          startIndex = startEnd[0];
+          endIndex = startEnd[1];
+          // get first non-gaped residue start position
+          while (jalview.util.Comparison.isGap(seqs[i]
+                  .getCharAt(startIndex)) && startIndex < endIndex)
+          {
+            startIndex++;
+          }
+
+          // get last non-gaped residue end position
+          while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex))
+                  && endIndex > startIndex)
+          {
+            endIndex--;
+          }
+
+          startRes = seqs[i].findPosition(startIndex);
+          endRes = seqs[i].findPosition(endIndex);
+        }
+
         tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
-                seqs[i].getStart(), seqs[i].getEnd());
+                startRes, endRes);
         tmp[i].setDescription(seqs[i].getDescription());
       }
       seqs = tmp;
@@ -168,16 +236,17 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, ColumnSelection colSel)
+          String[] omitHidden, int[] exportRange, ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden,
+    return formatSequences(format, alignment, omitHidden, exportRange,
             getCacheSuffixDefault(format), colSel, null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+          String[] omitHidden, int[] exportRange, ColumnSelection colSel,
+          SequenceGroup sgp)
   {
-    return formatSequences(format, alignment, omitHidden,
+    return formatSequences(format, alignment, omitHidden, exportRange,
             getCacheSuffixDefault(format), colSel, sgp);
   }
 
@@ -194,15 +263,16 @@ public class FormatAdapter extends AppletFormatAdapter
    * @return string representation of the alignment formatted as format
    */
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, boolean suffix, ColumnSelection colSel)
+          String[] omitHidden, int[] exportRange, boolean suffix,
+          ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden, suffix, colSel,
-            null);
+    return formatSequences(format, alignment, omitHidden, exportRange,
+            suffix, colSel, null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, boolean suffix, ColumnSelection colSel,
-          jalview.datamodel.SequenceGroup selgp)
+          String[] omitHidden, int[] exportRange, boolean suffix,
+          ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
   {
     if (omitHidden != null)
     {
@@ -211,7 +281,7 @@ public class FormatAdapter extends AppletFormatAdapter
       // TODO: JAL-1486 - set start and end for output correctly. basically,
       // AlignmentView.getVisibleContigs does this.
       Alignment alv = new Alignment(replaceStrings(
-              alignment.getSequencesArray(), omitHidden));
+              alignment.getSequencesArray(), omitHidden, exportRange));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
       if (ala != null)
       {
@@ -235,38 +305,17 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
-  public Alignment readFile(String inFile, String type, String format)
+  public AlignmentI readFile(String inFile, String type, String format)
           throws java.io.IOException
   {
-    Alignment al;
-    if (format.equals("HTML"))
-    {
-      afile = new HtmlFile(inFile, type);
-      al = new Alignment(afile.getSeqsAsArray());
-      afile.addAnnotations(al);
-    }
-    else
-    {
-      al = super.readFile(inFile, type, format);
-    }
-
+    AlignmentI al = super.readFile(inFile, type, format);
     return al;
   }
 
   public AlignmentI readFromFile(FileParse source, String format)
           throws java.io.IOException
   {
-    Alignment al;
-    if (format.equals("HTML"))
-    {
-      afile = new HtmlFile(source);
-      al = new Alignment(afile.getSeqsAsArray());
-      afile.addAnnotations(al);
-    }
-    else
-    {
-      al = (Alignment) super.readFromFile(source, format);
-    }
+    AlignmentI al = super.readFromFile(source, format);
     return al;
   }
 
@@ -293,14 +342,19 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   /**
-   * Create a flat file representation of a given view or selected region of a view
+   * Create a flat file representation of a given view or selected region of a
+   * view
+   * 
    * @param format
-   * @param av
+   * @param ap
+   *          alignment panel originating the view
    * @return String containing flat file
    */
-  public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+  public String formatSequences(String format, AlignmentViewPanel ap,
+          boolean selectedOnly)
   {
-    return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+    return formatSequences(format, getCacheSuffixDefault(format), ap,
+            selectedOnly);
   }
 
 }