Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/datamodel/Profile.java b/src/jalview/datamodel/Profile.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;
+
+
+/**
+ * A profile for one column of an alignment
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class Profile implements ProfileI
+{
+  /*
+   * an object holding counts of symbols in the profile
+   */
+  private ResidueCount counts;
+
+  /*
+   * the number of sequences (gapped or not) in the profile
+   */
+  private int height;
+
+  /*
+   * the number of non-gapped sequences in the profile
+   */
+  private int gapped;
+
+  /*
+   * the highest count for any residue in the profile
+   */
+  private int maxCount;
+
+  /*
+   * the residue (e.g. K) or residues (e.g. KQW) with the
+   * highest count in the profile
+   */
+  private String modalResidue;
+
+  /**
+   * Constructor which allows derived data to be stored without having to store
+   * the full profile
+   * 
+   * @param seqCount
+   *          the number of sequences in the profile
+   * @param gaps
+   *          the number of gapped sequences
+   * @param max
+   *          the highest count for any residue
+   * @param modalres
+   *          the residue (or concatenated residues) with the highest count
+   */
+  public Profile(int seqCount, int gaps, int max, String modalRes)
+  {
+    this.height = seqCount;
+    this.gapped = gaps;
+    this.maxCount = max;
+    this.modalResidue = modalRes;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#setCounts(jalview.datamodel.ResidueCount)
+   */
+  @Override
+  public void setCounts(ResidueCount residueCounts)
+  {
+    this.counts = residueCounts;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getPercentageIdentity(boolean)
+   */
+  @Override
+  public float getPercentageIdentity(boolean ignoreGaps)
+  {
+    if (height == 0)
+    {
+      return 0f;
+    }
+    float pid = 0f;
+    if (ignoreGaps && gapped < height)
+    {
+      pid = (maxCount * 100f) / (height - gapped);
+    }
+    else
+    {
+      pid = (maxCount * 100f) / height;
+    }
+    return pid;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getCounts()
+   */
+  @Override
+  public ResidueCount getCounts()
+  {
+    return counts;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getHeight()
+   */
+  @Override
+  public int getHeight()
+  {
+    return height;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getGapped()
+   */
+  @Override
+  public int getGapped()
+  {
+    return gapped;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getMaxCount()
+   */
+  @Override
+  public int getMaxCount()
+  {
+    return maxCount;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getModalResidue()
+   */
+  @Override
+  public String getModalResidue()
+  {
+    return modalResidue;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getNonGapped()
+   */
+  @Override
+  public int getNonGapped()
+  {
+    return height - gapped;
+  }
+}