utility functions for dealing with Range and Properties elements.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@353 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/objects/utils/Properties.java b/src/uk/ac/vamsas/objects/utils/Properties.java
new file mode 100644 (file)
index 0000000..491a781
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/Properties.java
@@ -0,0 +1,21 @@
+package uk.ac.vamsas.objects.utils;\r
+\r
+import uk.ac.vamsas.objects.core.Property;\r
+\r
+public class Properties {\r
+  public static Property newProperty(String name, String type, String content)\r
+  {\r
+    Property vProperty = new Property();\r
+    vProperty.setName(name);\r
+    if (type != null)\r
+    {\r
+      vProperty.setType(type);\r
+    }\r
+    else\r
+    {\r
+      vProperty.setType("String");\r
+    }\r
+    vProperty.setContent(content);\r
+    return vProperty;\r
+  }\r
+}\r

diff --git a/src/uk/ac/vamsas/objects/utils/Range.java b/src/uk/ac/vamsas/objects/utils/Range.java
new file mode 100644 (file)
index 0000000..b20cb5b
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/Range.java
@@ -0,0 +1,146 @@
+package uk.ac.vamsas.objects.utils;\r
+\r
+import java.util.Vector;\r
+\r
+\r
+import uk.ac.vamsas.objects.core.RangeType;\r
+import uk.ac.vamsas.objects.core.Seg;\r
+\r
+public class Range {\r
+\r
+  /**\r
+   * get start<end range of segment, adjusting for inclusivity flag and\r
+   * polarity.\r
+   *\r
+   * @param visSeg\r
+   * @param ensureDirection when true - always ensure start is less than end.\r
+   * @return int[] { start, end, direction} where direction==1 for range running from end to start.\r
+   */\r
+  public static int[] getSegRange(Seg visSeg, boolean ensureDirection)\r
+  {\r
+    boolean incl = visSeg.getInclusive();\r
+    // adjust for inclusive flag.\r
+    int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of\r
+    // region.\r
+    int start = visSeg.getStart() + (incl ? 0 : pol);\r
+    int end = visSeg.getEnd() + (incl ? 0 : -pol);\r
+    if (ensureDirection && pol == -1)\r
+    {\r
+      // jalview doesn't deal with inverted ranges, yet.\r
+      int t = end;\r
+      end = start;\r
+      start = t;\r
+    }\r
+    return new int[]\r
+        {\r
+        start, end, pol < 0 ? 1 : 0};\r
+  }\r
+\r
+  /**\r
+   * get real bounds of a RangeType's specification. start and end are an\r
+   * inclusive range within which all segments and positions lie.\r
+   * TODO: refactor to vamsas utils\r
+   * @param dseta\r
+   * @return int[] { start, end}\r
+   */\r
+  public static int[] getBounds(RangeType dseta)\r
+  {\r
+    if (dseta != null)\r
+    {\r
+      int[] se = null;\r
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)\r
+      {\r
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+      }\r
+      if (dseta.getSegCount() > 0)\r
+      {\r
+        se = getSegRange(dseta.getSeg(0), true);\r
+        for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)\r
+        {\r
+          int nse[] = getSegRange(dseta.getSeg(s), true);\r
+          if (se[0] > nse[0])\r
+          {\r
+            se[0] = nse[0];\r
+          }\r
+          if (se[1] < nse[1])\r
+          {\r
+            se[1] = nse[1];\r
+          }\r
+        }\r
+      }\r
+      if (dseta.getPosCount() > 0)\r
+      {\r
+        // could do a polarity for pos range too. and pass back indication of discontinuities.\r
+        int pos = dseta.getPos(0).getI();\r
+        se = new int[]\r
+            {\r
+            pos, pos};\r
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
+        {\r
+          pos = dseta.getPos(p).getI();\r
+          if (se[0] > pos)\r
+          {\r
+            se[0] = pos;\r
+          }\r
+          if (se[1] < pos)\r
+          {\r
+            se[1] = pos;\r
+          }\r
+        }\r
+      }\r
+      return se;\r
+    }\r
+    return null;\r
+  }\r
+\r
+  /**\r
+   * map from a rangeType's internal frame to the referenced object's coordinate frame.\r
+   * @param dseta\r
+   * @return int [] { ref(pos)...} for all pos in rangeType's frame.\r
+   */\r
+  public static int[] getMapping(RangeType dseta)\r
+  {\r
+    Vector posList = new Vector();\r
+    if (dseta != null)\r
+    {\r
+      int[] se = null;\r
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)\r
+      {\r
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+      }\r
+      if (dseta.getSegCount() > 0)\r
+      {\r
+        for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)\r
+        {\r
+          se = getSegRange(dseta.getSeg(s), false);\r
+          int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);\r
+          for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)\r
+          {\r
+            posList.add(new Integer(p));\r
+          }\r
+        }\r
+      }\r
+      else if (dseta.getPosCount() > 0)\r
+      {\r
+        int pos = dseta.getPos(0).getI();\r
+\r
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
+        {\r
+          pos = dseta.getPos(p).getI();\r
+          posList.add(new Integer(pos));\r
+        }\r
+      }\r
+    }\r
+    if (posList != null && posList.size() > 0)\r
+    {\r
+      int[] range = new int[posList.size()];\r
+      for (int i = 0; i < range.length; i++)\r
+      {\r
+        range[i] = ( (Integer) posList.elementAt(i)).intValue();\r
+      }\r
+      posList.clear();\r
+      return range;\r
+    }\r
+    return null;\r
+  }\r
+}\r