after merge

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 60ad85c..2fd1773 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -69,8 +69,8 @@ public class AlignSeq
     int maxj;\r
     int[] aseq1;\r
     int[] aseq2;\r
-    String astr1 = "";\r
-    String astr2 = "";\r
+    public String astr1 = "";\r
+    public String astr2 = "";\r
 \r
     /** DOCUMENT ME!! */\r
     public int seq1start;\r
@@ -94,7 +94,7 @@ public class AlignSeq
     int[][] lookup = ResidueProperties.getBLOSUM62();\r
     String[] intToStr = pep;\r
     int defInt = 23;\r
-    String output = "";\r
+    StringBuffer output = new StringBuffer();\r
     String type;\r
     Runtime rt;\r
 \r
@@ -169,7 +169,7 @@ public class AlignSeq
      */\r
     public String getOutput()\r
     {\r
-        return output;\r
+        return output.toString();\r
     }\r
 \r
     /**\r
@@ -263,7 +263,7 @@ public class AlignSeq
         }\r
         else\r
         {\r
-            output = output + ("Wrong type = dna or pep only");\r
+            output.append("Wrong type = dna or pep only");\r
             System.exit(0);\r
         }\r
 \r
@@ -406,7 +406,7 @@ public class AlignSeq
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void printAlignment()\r
+    public void printAlignment(java.io.PrintStream os)\r
     {\r
         // Find the biggest id length for formatting purposes\r
         int maxid = s1.getName().length();\r
@@ -420,39 +420,33 @@ public class AlignSeq
         int nochunks = ((aseq1.length - count) / len) + 1;\r
         pid = 0;\r
 \r
-        output = output + ("Score = " + score[maxi][maxj] + "\n");\r
-        output = output +\r
-            ("Length of alignment = " + (aseq1.length - count) + "\n");\r
-        output = output + ("Sequence ");\r
-        output = output + (new Format("%" + maxid + "s").form(s1.getName()));\r
-        output = output +\r
-            (" :  " + seq1start + " - " + seq1end + " (Sequence length = " +\r
+        output.append("Score = " + score[maxi][maxj] + "\n");\r
+        output.append("Length of alignment = " + (aseq1.length - count) + "\n");\r
+        output.append("Sequence ");\r
+        output.append(new Format("%" + maxid + "s").form(s1.getName()));\r
+        output.append(" :  " + seq1start + " - " + seq1end + " (Sequence length = " +\r
             s1str.length() + ")\n");\r
-        output = output + ("Sequence ");\r
-        output = output + (new Format("%" + maxid + "s").form(s2.getName()));\r
-        output = output +\r
-            (" :  " + seq2start + " - " + seq2end + " (Sequence length = " +\r
+        output .append("Sequence ");\r
+        output.append(new Format("%" + maxid + "s").form(s2.getName()));\r
+        output .append(" :  " + seq2start + " - " + seq2end + " (Sequence length = " +\r
             s2str.length() + ")\n\n");\r
 \r
         for (int j = 0; j < nochunks; j++)\r
         {\r
             // Print the first aligned sequence\r
-            output = output +\r
-                (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");\r
+            output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");\r
 \r
             for (int i = 0; i < len; i++)\r
             {\r
                 if ((count + i + (j * len)) < aseq1.length)\r
                 {\r
-                    output = output +\r
-                        (new Format("%s").form(intToStr[aseq1[count + i +\r
+                    output.append(new Format("%s").form(intToStr[aseq1[count + i +\r
                             (j * len)]]));\r
                 }\r
             }\r
 \r
-            output = output + ("\n");\r
-            output = output +\r
-                (new Format("%" + (maxid) + "s").form(" ") + " ");\r
+            output.append("\n");\r
+            output.append(new Format("%" + (maxid) + "s").form(" ") + " ");\r
 \r
             // Print out the matching chars\r
             for (int i = 0; i < len; i++)\r
@@ -464,7 +458,7 @@ public class AlignSeq
                             !intToStr[aseq1[count + i + (j * len)]].equals("-"))\r
                     {\r
                         pid++;\r
-                        output = output + ("|");\r
+                        output.append("|");\r
                     }\r
                     else if (type.equals("pep"))\r
                     {\r
@@ -472,40 +466,42 @@ public class AlignSeq
                                     intToStr[aseq1[count + i + (j * len)]],\r
                                     intToStr[aseq2[count + i + (j * len)]]) > 0)\r
                         {\r
-                            output = output + (".");\r
+                            output.append(".");\r
                         }\r
                         else\r
                         {\r
-                            output = output + (" ");\r
+                            output.append(" ");\r
                         }\r
                     }\r
                     else\r
                     {\r
-                        output = output + (" ");\r
+                        output.append(" ");\r
                     }\r
                 }\r
             }\r
 \r
             // Now print the second aligned sequence\r
-            output = output + ("\n");\r
-            output = output +\r
-                (new Format("%" + (maxid) + "s").form(s2.getName()) + " ");\r
+            output = output.append("\n");\r
+            output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " ");\r
 \r
             for (int i = 0; i < len; i++)\r
             {\r
                 if ((count + i + (j * len)) < aseq1.length)\r
                 {\r
-                    output = output +\r
-                        (new Format("%s").form(intToStr[aseq2[count + i +\r
+                    output .append(new Format("%s").form(intToStr[aseq2[count + i +\r
                             (j * len)]]));\r
                 }\r
             }\r
 \r
-            output = output + ("\n\n");\r
+            output = output .append("\n\n");\r
         }\r
 \r
         pid = pid / (float) (aseq1.length - count) * 100;\r
-        output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));\r
+        output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));\r
+\r
+        try{\r
+          os.println(output.toString());\r
+        }catch(Exception ex){}\r
     }\r
 \r
     /**\r
@@ -659,14 +655,14 @@ public class AlignSeq
     public static String extractGaps(String gapChar, String seq)\r
     {\r
         StringTokenizer str = new StringTokenizer(seq, gapChar);\r
-        String newString = "";\r
+        StringBuffer newString = new StringBuffer();\r
 \r
         while (str.hasMoreTokens())\r
         {\r
-            newString = newString + str.nextToken();\r
+            newString.append( str.nextToken() );\r
         }\r
 \r
-        return newString;\r
+        return newString.toString();\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 99592f2..0683265 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -18,13 +18,16 @@
 */\r
 package jalview.analysis;\r
 \r
-import java.util.*;\r
-\r
 import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
+\r
+import jalview.io.NewickFile;\r
+\r
+import jalview.schemes.ResidueProperties;\r
+\r
 import jalview.util.*;\r
 \r
+import java.util.*;\r
+\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -57,10 +60,6 @@ public class NJTree
     Object leaves = null;\r
     int start;\r
     int end;\r
-    boolean hasDistances = true; // normal case for jalview trees\r
-    boolean hasBootstrap = false; // normal case for jalview trees\r
-\r
-  private boolean hasRootDistance = true;\r
 \r
     /**\r
      * Creates a new NJTree object.\r
@@ -82,11 +81,6 @@ public class NJTree
     public NJTree(SequenceI[] seqs, NewickFile treefile)\r
     {\r
         top = treefile.getTree();\r
-\r
-        hasDistances = treefile.HasDistances();\r
-        hasBootstrap = treefile.HasBootstrap();\r
-        hasRootDistance = treefile.HasRootDistance();\r
-\r
         maxheight = findHeight(top);\r
 \r
         SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
@@ -664,7 +658,7 @@ public class NJTree
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");\r
                     as.calcScoreMatrix();\r
                     as.traceAlignment();\r
-                    as.printAlignment();\r
+                    as.printAlignment(System.out);\r
                     distance[i][j] = (float) as.maxscore;\r
 \r
                     if (max < distance[i][j])\r
@@ -1140,27 +1134,6 @@ public class NJTree
     {\r
         return top;\r
     }\r
-    /**\r
-     *\r
-     * @return true if tree has real distances\r
-     */\r
-    public boolean isHasDistances() {\r
-      return hasDistances;\r
-    }\r
-\r
-    /**\r
-     *\r
-     * @return true if tree has real bootstrap values\r
-     */\r
-    public boolean isHasBootstrap() {\r
-      return hasBootstrap;\r
-    }\r
-\r
-  public boolean isHasRootDistance()\r
-  {\r
-    return hasRootDistance;\r
-  }\r
-\r
 }\r
 \r
 \r

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index bd0f45c..564e3f1 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -49,10 +49,10 @@ public class SeqsetUtils
     sqinfo.put("Name", seq.getName());\r
     sqinfo.put("Start", new Integer(seq.getStart()));\r
     sqinfo.put("End", new Integer(seq.getEnd()));\r
-    sqinfo.put("SeqFeatures", seq.getSequenceFeatures());\r
+    sqinfo.put("SeqFeatures", (seq.getSequenceFeatures() !=null) ? seq.getSequenceFeatures() : new Vector());\r
     sqinfo.put("PdbId",\r
-               (seq.getPDBId() != null) ? seq.getPDBId() : new String(""));\r
-\r
+               (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());\r
+    sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));\r
     return sqinfo;\r
   }\r
 \r
@@ -71,8 +71,8 @@ public class SeqsetUtils
     Integer end = (Integer) sqinfo.get("End");\r
     java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(\r
         "SeqFeatures");\r
-    String pdbid = (String) sqinfo.get("PdbId");\r
-\r
+    Vector pdbid = (Vector) sqinfo.get("PdbId");\r
+    Sequence seqds = (Sequence) sqinfo.get("datasetSequence");\r
     if (oldname == null)\r
     {\r
       namePresent = false;\r
@@ -93,10 +93,13 @@ public class SeqsetUtils
       sq.setEnd(end.intValue());\r
     }\r
 \r
-    if (sfeatures != null)\r
+    if ((sfeatures != null) && (sfeatures.size()>0))\r
     {\r
       sq.setSequenceFeatures(sfeatures);\r
     }\r
+    if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {\r
+      sq.setDatasetSequence(seqds);\r
+    }\r
 \r
     return namePresent;\r
   }\r