--- /dev/null
+/*
+ * 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.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+
+import jalview.bin.Console;
+
+public abstract class ContactMatrix extends GroupSetHolder
+ implements ContactMatrixI
+{
+ /**
+ * are contacts reflexive ?
+ */
+ boolean symmetric = true;
+
+ public ContactMatrix(boolean symmetric)
+ {
+ this.symmetric = symmetric;
+ }
+
+ List<List<Float>> contacts = null;
+
+ int width = 0, numcontacts = 0;
+
+ float min = 0f, max = 0f;
+
+ public void addContact(int left, int right, float strength)
+ {
+ if (left < 0 || right < 0)
+ {
+ throw new Error(new RuntimeException(
+ "Cannot have negative indices for contact left=" + left
+ + " right=" + right + " strength=" + strength));
+ }
+ if (symmetric)
+ {
+ if (left > right)
+ {
+ // swap
+ int r = right;
+ right = left;
+ left = r;
+ }
+ }
+ if (contacts == null)
+ {
+ // TODO: use sparse list for efficiency ?
+ contacts = new ArrayList<List<Float>>();
+ }
+ List<Float> clist = contacts.get(left);
+ if (clist == null)
+ {
+ clist = new ArrayList<Float>();
+ contacts.set(left, clist);
+ }
+ Float last = clist.set(right, strength);
+ // TODO: if last is non null, may need to recompute range
+ checkBounds(strength);
+ if (last == null)
+ {
+ numcontacts++;
+ }
+ }
+
+ private void checkBounds(float strength)
+ {
+ if (min > strength)
+ {
+ min = strength;
+ }
+ if (max < strength)
+ {
+ max = strength;
+ }
+ }
+
+ @Override
+ public ContactListI getContactList(final int column)
+ {
+ if (column < 0 || column >= width)
+ {
+ return null;
+ }
+
+ return new ContactListImpl(new ContactListProviderI()
+ {
+ int p = column;
+
+ @Override
+ public int getPosition()
+ {
+ return p;
+ }
+
+ @Override
+ public int getContactHeight()
+ {
+ return width;
+
+ }
+
+ @Override
+ public double getContactAt(int column)
+ {
+ Float cl = getFloatElementAt(column, p);
+ if (cl == null)
+ {
+ // return 0 not NaN ?
+ return Double.NaN;
+ }
+ return cl.doubleValue();
+ }
+ });
+ }
+
+ private Float getFloatElementAt(int column, int p)
+ {
+
+ 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 double getElementAt(int column, int row)
+ {
+ Float cl = getFloatElementAt(column, row);
+ if (cl != null)
+ {
+ return cl;
+ }
+ throw (new RuntimeException("Out of Bounds " + column + "," + row));
+ }
+
+ @Override
+ public float getMin()
+ {
+ return min;
+ }
+
+ @Override
+ public float getMax()
+ {
+ return max;
+ }
+
+ @Override
+ public String getAnnotLabel()
+ {
+ return "Contact Matrix";
+ }
+
+ @Override
+ public String getAnnotDescr()
+ {
+ return "Contact Matrix";
+ }
+
+ 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)
+ {
+ if (sb.length() - lastsb > 320)
+ {
+ // newline
+ sb.append('\n');
+ lastsb = sb.length();
+ }
+ else
+ {
+ sb.append('\t');
+ }
+ }
+ sb.append(cl.getContactAt(h));
+ }
+ }
+ }
+ return sb.toString();
+ }
+
+ public static float[][] fromFloatStringToContacts(String values, int cols,
+ int rows)
+ {
+ float[][] vals = new float[cols][rows];
+ StringTokenizer tabsep = new StringTokenizer(values, "" + '\t' + '\n');
+ int c = 0, r = 0;
+ while (tabsep.hasMoreTokens())
+ {
+ double elem = Double.valueOf(tabsep.nextToken());
+ vals[c][r++] = (float) elem;
+ if (r >= vals[c].length)
+ {
+ r = 0;
+ c++;
+ }
+ if (c >= vals.length)
+ {
+ break;
+ }
+ }
+ if (tabsep.hasMoreElements())
+ {
+ Console.warn(
+ "Ignoring additional elements for Float string to contact matrix parsing.");
+ }
+ return vals;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff