+/*
+ * 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 java.util.ArrayList;
-import java.util.BitSet;
-import java.util.HashMap;
import java.util.List;
import java.util.StringTokenizer;
import jalview.bin.Console;
-public abstract class ContactMatrix implements ContactMatrixI
+public abstract class ContactMatrix extends GroupSetHolder
+ implements ContactMatrixI
{
/**
* are contacts reflexive ?
@Override
public double getContactAt(int column)
{
- List<Float> clist;
- Float cl = null;
- if (symmetric)
- {
- if (p < column)
- {
- clist = contacts.get(p);
- cl = clist.get(column);
- }
- else
- {
- clist = contacts.get(column);
- cl = clist.get(p);
- }
- }
- else
- {
- clist = contacts.get(p);
- cl = clist.get(column);
- }
+ Float cl = getFloatElementAt(column, p);
if (cl == null)
{
// return 0 not NaN ?
});
}
- @Override
- public float getMin()
+ private Float getFloatElementAt(int column, int p)
{
- return min;
+
+ List<Float> clist;
+ Float cl = null;
+ if (symmetric)
+ {
+ if (p < column)
+ {
+ clist = contacts.get(p);
+ cl = clist.get(column);
+ }
+ else
+ {
+ clist = contacts.get(column);
+ cl = clist.get(p);
+ }
+ }
+ else
+ {
+ clist = contacts.get(p);
+ cl = clist.get(column);
+ }
+ return cl;
}
@Override
- public float getMax()
+ public double getElementAt(int column, int row)
{
- return max;
+ Float cl = getFloatElementAt(column, row);
+ if (cl != null)
+ {
+ return cl;
+ }
+ throw (new RuntimeException("Out of Bounds " + column + "," + row));
}
@Override
- public boolean hasReferenceSeq()
+ public float getMin()
{
- // TODO Auto-generated method stub
- return false;
+ return min;
}
@Override
- public SequenceI getReferenceSeq()
+ public float getMax()
{
- // TODO Auto-generated method stub
- return null;
+ return max;
}
@Override
return "Contact Matrix";
}
- List<BitSet> groups = null;
-
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- colorMap = new HashMap<>();
- }
-
- @Override
- public boolean hasGroups()
- {
- return groups != null && groups.size() > 0;
- }
-
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- @Override
- public BitSet getGroupsFor(int column)
- {
- for (BitSet gp : groups)
- {
- if (gp.get(column))
- {
- return gp;
- }
- }
- return ContactMatrixI.super.getGroupsFor(column);
- }
-
- HashMap<BitSet, Color> colorMap = new HashMap<>();
-
- @Override
- public Color getColourForGroup(BitSet bs)
- {
- if (bs == null)
- {
- return Color.white;
- }
- Color groupCol = colorMap.get(bs);
- if (groupCol == null)
- {
- return Color.white;
- }
- return groupCol;
- }
-
- @Override
- public void setColorForGroup(BitSet bs, Color color)
- {
- colorMap.put(bs, color);
- }
-
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
for (int c = 0; c < cm.getWidth(); c++)
{
ContactListI cl = cm.getContactList(c);
+ long lastsb = -1;
if (cl != null)
{
for (int h = 0; h <= cl.getContactHeight(); h++)
{
if (sb.length() > 0)
{
- sb.append('\t');
+ if (sb.length() - lastsb > 320)
+ {
+ // newline
+ sb.append('\n');
+ lastsb = sb.length();
+ }
+ else
+ {
+ sb.append('\t');
+ }
}
sb.append(cl.getContactAt(h));
}
int rows)
{
float[][] vals = new float[cols][rows];
- StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+ StringTokenizer tabsep = new StringTokenizer(values, "" + '\t' + '\n');
int c = 0, r = 0;
-
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
}
if (c >= vals.length)
{
-
break;
}
}
Console.warn(
"Ignoring additional elements for Float string to contact matrix parsing.");
}
-
return vals;
}
}
git://source.jalview.org / jalview.git / blobdiff