JAL-1551 remove temp file in src

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

diff --git a/src/jalview/datamodel/Profile.java~ b/src/jalview/datamodel/Profile.java~
deleted file mode 100644 (file)
index 5464596..0000000
--- a/src/jalview/datamodel/Profile.java~
+++ /dev/null
@@ -1,143 +0,0 @@
-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;
-  }
-}