X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrix.java;h=b8593d842fd8474487f96ae14e3fe4b6dea82e26;hb=b028e684c807365decd0c6e6111aa4bf368a6fa8;hp=25aefd3851dd04bdc6e5672449f70606c93cf68d;hpb=a0ac724dba7d556966b546d4a0093449c397be84;p=jalview.git
diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 25aefd3..b8593d8 100644
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,3 +1,23 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.util.ArrayList;
@@ -6,7 +26,8 @@ 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 ?
@@ -102,26 +123,7 @@ public abstract class ContactMatrix implements ContactMatrixI
@Override
public double getContactAt(int column)
{
- List 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 ?
@@ -132,30 +134,53 @@ public abstract class ContactMatrix implements ContactMatrixI
});
}
- @Override
- public float getMin()
+ private Float getFloatElementAt(int column, int p)
{
- return min;
+
+ List 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
@@ -176,13 +201,23 @@ public abstract class ContactMatrix implements ContactMatrixI
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));
}
@@ -195,9 +230,8 @@ public abstract class ContactMatrix implements ContactMatrixI
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());
@@ -209,7 +243,6 @@ public abstract class ContactMatrix implements ContactMatrixI
}
if (c >= vals.length)
{
-
break;
}
}
@@ -218,7 +251,6 @@ public abstract class ContactMatrix implements ContactMatrixI
Console.warn(
"Ignoring additional elements for Float string to contact matrix parsing.");
}
-
return vals;
}
}