From aab514f0d55b43f9f4f5154e3e34103c1b41becc Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 8 Mar 2007 14:07:22 +0000
Subject: [PATCH] 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
---
 src/uk/ac/vamsas/objects/utils/Properties.java |   21 ++++
 src/uk/ac/vamsas/objects/utils/Range.java      |  146 ++++++++++++++++++++++++
 2 files changed, 167 insertions(+)
 create mode 100644 src/uk/ac/vamsas/objects/utils/Properties.java
 create mode 100644 src/uk/ac/vamsas/objects/utils/Range.java

diff --git a/src/uk/ac/vamsas/objects/utils/Properties.java b/src/uk/ac/vamsas/objects/utils/Properties.java
new file mode 100644
index 0000000..491a781
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/Properties.java
@@ -0,0 +1,21 @@
+package uk.ac.vamsas.objects.utils;
+
+import uk.ac.vamsas.objects.core.Property;
+
+public class Properties {
+  public static Property newProperty(String name, String type, String content)
+  {
+    Property vProperty = new Property();
+    vProperty.setName(name);
+    if (type != null)
+    {
+      vProperty.setType(type);
+    }
+    else
+    {
+      vProperty.setType("String");
+    }
+    vProperty.setContent(content);
+    return vProperty;
+  }
+}
diff --git a/src/uk/ac/vamsas/objects/utils/Range.java b/src/uk/ac/vamsas/objects/utils/Range.java
new file mode 100644
index 0000000..b20cb5b
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/Range.java
@@ -0,0 +1,146 @@
+package uk.ac.vamsas.objects.utils;
+
+import java.util.Vector;
+
+
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+
+public class Range {
+
+  /**
+   * get start<end range of segment, adjusting for inclusivity flag and
+   * polarity.
+   *
+   * @param visSeg
+   * @param ensureDirection when true - always ensure start is less than end.
+   * @return int[] { start, end, direction} where direction==1 for range running from end to start.
+   */
+  public static int[] getSegRange(Seg visSeg, boolean ensureDirection)
+  {
+    boolean incl = visSeg.getInclusive();
+    // adjust for inclusive flag.
+    int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
+    // region.
+    int start = visSeg.getStart() + (incl ? 0 : pol);
+    int end = visSeg.getEnd() + (incl ? 0 : -pol);
+    if (ensureDirection && pol == -1)
+    {
+      // jalview doesn't deal with inverted ranges, yet.
+      int t = end;
+      end = start;
+      start = t;
+    }
+    return new int[]
+        {
+        start, end, pol < 0 ? 1 : 0};
+  }
+
+  /**
+   * get real bounds of a RangeType's specification. start and end are an
+   * inclusive range within which all segments and positions lie.
+   * TODO: refactor to vamsas utils
+   * @param dseta
+   * @return int[] { start, end}
+   */
+  public static int[] getBounds(RangeType dseta)
+  {
+    if (dseta != null)
+    {
+      int[] se = null;
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+      {
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      }
+      if (dseta.getSegCount() > 0)
+      {
+        se = getSegRange(dseta.getSeg(0), true);
+        for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
+        {
+          int nse[] = getSegRange(dseta.getSeg(s), true);
+          if (se[0] > nse[0])
+          {
+            se[0] = nse[0];
+          }
+          if (se[1] < nse[1])
+          {
+            se[1] = nse[1];
+          }
+        }
+      }
+      if (dseta.getPosCount() > 0)
+      {
+        // could do a polarity for pos range too. and pass back indication of discontinuities.
+        int pos = dseta.getPos(0).getI();
+        se = new int[]
+            {
+            pos, pos};
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
+        {
+          pos = dseta.getPos(p).getI();
+          if (se[0] > pos)
+          {
+            se[0] = pos;
+          }
+          if (se[1] < pos)
+          {
+            se[1] = pos;
+          }
+        }
+      }
+      return se;
+    }
+    return null;
+  }
+
+  /**
+   * map from a rangeType's internal frame to the referenced object's coordinate frame.
+   * @param dseta
+   * @return int [] { ref(pos)...} for all pos in rangeType's frame.
+   */
+  public static int[] getMapping(RangeType dseta)
+  {
+    Vector posList = new Vector();
+    if (dseta != null)
+    {
+      int[] se = null;
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+      {
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      }
+      if (dseta.getSegCount() > 0)
+      {
+        for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
+        {
+          se = getSegRange(dseta.getSeg(s), false);
+          int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
+          for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
+          {
+            posList.add(new Integer(p));
+          }
+        }
+      }
+      else if (dseta.getPosCount() > 0)
+      {
+        int pos = dseta.getPos(0).getI();
+
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
+        {
+          pos = dseta.getPos(p).getI();
+          posList.add(new Integer(pos));
+        }
+      }
+    }
+    if (posList != null && posList.size() > 0)
+    {
+      int[] range = new int[posList.size()];
+      for (int i = 0; i < range.length; i++)
+      {
+        range[i] = ( (Integer) posList.elementAt(i)).intValue();
+      }
+      posList.clear();
+      return range;
+    }
+    return null;
+  }
+}
-- 
1.7.10.2