Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / datamodel / ContactListImpl.java

diff --git a/src/jalview/datamodel/ContactListImpl.java b/src/jalview/datamodel/ContactListImpl.java
new file mode 100644 (file)
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--- /dev/null
+++ b/src/jalview/datamodel/ContactListImpl.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.awt.Color;
+
+import jalview.renderer.ContactGeometry.contactInterval;
+
+/**
+ * helper class to compute min/max/mean for a range on a contact list
+ * 
+ * @author jprocter
+ *
+ */
+public class ContactListImpl implements ContactListI
+{
+  ContactListProviderI clist;
+
+  public static ContactListI newContactList(ContactListProviderI list)
+  {
+    return new ContactListImpl(list);
+  }
+
+  public ContactListImpl(ContactListProviderI list)
+  {
+    clist = list;
+  }
+
+  @Override
+  public int getPosition()
+  {
+    return clist.getPosition();
+  }
+
+  @Override
+  public double getContactAt(int column)
+  {
+    return clist.getContactAt(column);
+  }
+
+  @Override
+  public int getContactHeight()
+  {
+    return clist.getContactHeight();
+  }
+
+  @Override
+  public ContactRange getRangeFor(int from_column, int to_column)
+  {
+    // TODO: consider caching ContactRange for a particular call ?
+    if (clist instanceof ContactListI)
+    {
+      // clist may implement getRangeFor in a more efficient way, so use theirs
+      return ((ContactListI) clist).getRangeFor(from_column, to_column);
+    }
+    if (from_column < 0)
+    {
+      from_column = 0;
+    }
+    if (to_column >= getContactHeight())
+    {
+      to_column = getContactHeight() - 1;
+    }
+    ContactRange cr = new ContactRange();
+    cr.setFrom_column(from_column);
+    cr.setTo_column(to_column);
+    double tot = 0;
+    for (int i = from_column; i <= to_column; i++)
+    {
+      double contact = getContactAt(i);
+      tot += contact;
+      if (i == from_column)
+      {
+        cr.setMin(contact);
+        cr.setMax(contact);
+        cr.setMinPos(i);
+        cr.setMaxPos(i);
+      }
+      else
+      {
+        if (cr.getMax() < contact)
+        {
+          cr.setMax(contact);
+          cr.setMaxPos(i);
+        }
+        if (cr.getMin() < contact)
+        {
+          cr.setMin(contact);
+          cr.setMinPos(i);
+        }
+      }
+    }
+    if (tot > 0 && to_column > from_column)
+    {
+      cr.setMean(tot / (1 + to_column - from_column));
+    }
+    else
+    {
+      cr.setMean(tot);
+    }
+    return cr;
+  }
+
+  @Override
+  public int[] getMappedPositionsFor(int cStart, int cEnd)
+  {
+    return clist.getMappedPositionsFor(cStart, cEnd);
+  }
+
+  @Override
+  public Color getColourForGroup()
+  {
+    return clist.getColourForGroup();
+  }
+}