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

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

diff --git a/src/jalview/datamodel/ProfileI.java b/src/jalview/datamodel/ProfileI.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;
+
+public interface ProfileI
+{
+
+  /**
+   * Set the full profile of counts
+   * 
+   * @param residueCounts
+   */
+  public abstract void setCounts(ResidueCount residueCounts);
+
+  /**
+   * Returns the percentage identity of the profile, i.e. the highest proportion
+   * of conserved (equal) symbols. The percentage is as a fraction of all
+   * sequences, or only ungapped sequences if flag ignoreGaps is set true.
+   * 
+   * @param ignoreGaps
+   * @return
+   */
+  public abstract float getPercentageIdentity(boolean ignoreGaps);
+
+  /**
+   * Returns the full symbol counts for this profile
+   * 
+   * @return
+   */
+  public abstract ResidueCount getCounts();
+
+  /**
+   * Returns the number of sequences in the profile
+   * 
+   * @return
+   */
+  public abstract int getHeight();
+
+  /**
+   * Returns the number of sequences in the profile which had a gap character
+   * (or were too short to be included in this column's profile)
+   * 
+   * @return
+   */
+  public abstract int getGapped();
+
+  /**
+   * Returns the highest count for any symbol(s) in the profile
+   * 
+   * @return
+   */
+  public abstract int getMaxCount();
+
+  /**
+   * Returns the symbol (or concatenated symbols) which have the highest count
+   * in the profile, or an empty string if there were no symbols counted
+   * 
+   * @return
+   */
+  public abstract String getModalResidue();
+
+  /**
+   * Answers the number of non-gapped sequences in the profile
+   * 
+   * @return
+   */
+  public abstract int getNonGapped();
+
+}
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