Container for VARNA classes are created according to Jmol classes.

[jalview.git] / src / jalview / ext / varna / VarnaCommands.java

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
new file mode 100644 (file)
index 0000000..9d57969
--- /dev/null
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -0,0 +1,142 @@
+/**\r
+ * \r
+ */\r
+package jalview.ext.varna;\r
+\r
+import jalview.api.FeatureRenderer;\r
+import jalview.api.SequenceRenderer;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.structure.StructureMapping;\r
+import jalview.structure.StructureSelectionManager;\r
+import jalview.util.Comparison;\r
+\r
+import java.awt.Color;\r
+import java.util.ArrayList;\r
+\r
+/**\r
+ * Routines for generating Jmol commands for Jalview/Jmol binding\r
+ * another cruisecontrol test.\r
+ * \r
+ * @author JimP\r
+ *\r
+ */\r
+public class VarnaCommands\r
+{\r
+\r
+  /**\r
+   * Jmol utility which constructs the commands to colour chains by the given alignment\r
+   * \r
+   */\r
+  public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
+  {\r
+    ArrayList<String> str = new ArrayList<String>();\r
+    StringBuffer command = new StringBuffer();\r
+  \r
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
+    {\r
+      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
+  \r
+      if (mapping == null || mapping.length < 1)\r
+        continue;\r
+  \r
+      int lastPos = -1;\r
+      for (int s = 0; s < sequence[pdbfnum].length; s++)\r
+      {\r
+        for (int sp, m = 0; m < mapping.length; m++)\r
+        {\r
+          if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
+                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
+          {\r
+            SequenceI asp = alignment.getSequenceAt(sp);\r
+            for (int r = 0; r < asp.getLength(); r++)\r
+            {\r
+              // no mapping to gaps in sequence\r
+              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
+              {\r
+                continue;\r
+              }\r
+              int pos = mapping[m].getPDBResNum(asp.findPosition(r));\r
+  \r
+              if (pos < 1 || pos == lastPos)\r
+                continue;\r
+  \r
+              lastPos = pos;\r
+  \r
+              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);\r
+  \r
+              if (fr != null)\r
+                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);\r
+              String newSelcom = (mapping[m].getChain() != " " ? ":"\r
+                      + mapping[m].getChain() : "")\r
+                      + "/"\r
+                      + (pdbfnum + 1)\r
+                      + ".1"\r
+                      + ";color["\r
+                      + col.getRed()\r
+                      + ","\r
+                      + col.getGreen()\r
+                      + ","\r
+                      + col.getBlue() + "]";\r
+              if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))\r
+              {\r
+                command = VarnaCommands.condenseCommand(command, pos);\r
+                continue;\r
+              }\r
+              // TODO: deal with case when buffer is too large for Jmol to parse\r
+              // - execute command and flush\r
+  \r
+              command.append(";");\r
+              if (command.length()>51200)\r
+              {\r
+                // add another chunk\r
+                str.add(command.toString());\r
+                command.setLength(0);\r
+              }\r
+              command.append("select " + pos);\r
+              command.append(newSelcom);\r
+            }\r
+            break;\r
+          }\r
+        }\r
+      }\r
+    }\r
+    {\r
+      // add final chunk\r
+      str.add(command.toString());\r
+      command.setLength(0);\r
+    }\r
+    return str.toArray(new String[str.size()]);\r
+  }\r
+\r
+  public static StringBuffer condenseCommand(StringBuffer command, int pos)\r
+  {\r
+  \r
+    // work back to last 'select'\r
+    int p=command.length(),q=p;\r
+    do {\r
+      p-=6;\r
+      if (p<1) { p=0; };\r
+    } while ((q=command.indexOf("select",p))==-1 && p>0);\r
+    \r
+    StringBuffer sb = new StringBuffer(command.substring(0,q+7));\r
+  \r
+    command =  command.delete(0,q+7);\r
+  \r
+    String start;\r
+  \r
+    if (command.indexOf("-") > -1)\r
+    {\r
+      start = command.substring(0, command.indexOf("-"));\r
+    }\r
+    else\r
+    {\r
+      start = command.substring(0, command.indexOf(":"));\r
+    }\r
+  \r
+    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));\r
+  \r
+    return sb;\r
+  }\r
+\r
+}\r