X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=64248c54aa07c66148028d3334811e66a85479fc;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=9cc74f11704bf10229f31c92e73ae8ec74bd0bf3;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 9cc74f1..64248c5 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,32 +1,165 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.schemes;
-
-import java.util.*;
-
-import java.awt.*;
-
-public interface ColourSchemeI
-{
- public Color findColour(String aa);
-
- public Color findColour(String s, int j);
-
- public void setConsensus(Vector v);
-}
+/*
+ * 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.schemes;
+
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+public interface ColourSchemeI
+{
+ /**
+ * Returns the colour for the given character. For use when the colour depends
+ * only on the symbol.
+ *
+ * @param c
+ * @return
+ */
+ Color findColour(char c);
+
+ /**
+ * Returns the possibly context dependent colour for the given symbol at the
+ * aligned position in the given sequence. For example, the colour may depend
+ * on the symbol's relationship to the consensus residue for the column.
+ *
+ * @param symbol
+ * @param position
+ * @param seq
+ * @return
+ */
+ Color findColour(char symbol, int position, SequenceI seq);
+
+ /**
+ * Assigns the given consensus profile for the colourscheme
+ */
+ void setConsensus(ProfilesI hconsensus);
+
+ /**
+ * Assigns the given conservation to the colourscheme
+ *
+ * @param c
+ */
+ void setConservation(Conservation c);
+
+ /**
+ * Enable or disable conservation shading for this colourscheme
+ *
+ * @param conservationApplied
+ */
+ void setConservationApplied(boolean conservationApplied);
+
+ /**
+ * Answers true if conservation shading is enabled for this colourscheme
+ *
+ * @return
+ */
+ boolean conservationApplied();
+
+ /**
+ * Sets the scale factor for bleaching of colour in unconserved regions
+ *
+ * @param i
+ */
+ void setConservationInc(int i);
+
+ /**
+ * Returns the scale factor for bleaching colour in unconserved regions
+ *
+ * @return
+ */
+ int getConservationInc();
+
+ /**
+ * Returns the percentage identity threshold for applying colourscheme
+ *
+ * @return
+ */
+ int getThreshold();
+
+ /**
+ * Sets the percentage identity threshold and type of %age identity
+ * calculation for shading
+ *
+ * @param pct
+ * 0..100 percentage identity for applying this colourscheme
+ * @param ignoreGaps
+ * when true, calculate PID without including gapped positions
+ */
+ void setThreshold(int pct, boolean ignoreGaps);
+
+ /**
+ * Recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
+ *
+ * @param alignment
+ * @param hiddenReps
+ */
+ void alignmentChanged(AnnotatedCollectionI alignment,
+ Map hiddenReps);
+
+ /**
+ * Creates and returns a new instance of the colourscheme configured to colour
+ * the given collection. Note that even simple colour schemes should return a
+ * new instance for each call to this method, as different instances may have
+ * differing shading by consensus or percentage identity applied.
+ *
+ * @param sg
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transferred
+ */
+ ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map hiddenRepSequences);
+
+ /**
+ * Answers true if the colour scheme is suitable for the given data, else
+ * false. For example, some colour schemes are specific to either peptide or
+ * nucleotide, or only apply if certain kinds of annotation are present.
+ *
+ * @param ac
+ * @return
+ */
+ // TODO can make this method static in Java 8
+ boolean isApplicableTo(AnnotatedCollectionI ac);
+
+ /**
+ * Answers the 'official' name of the colour scheme (as used, for example, as
+ * a Jalview startup parameter)
+ *
+ * @return
+ */
+ String getSchemeName();
+
+ /**
+ * Answers true if the colour scheme depends only on the sequence symbol, and
+ * not on other information such as alignment consensus or annotation. (Note
+ * that simple colour schemes may have a fading by percentage identity or
+ * conservation overlaid.) Simple colour schemes can be propagated to
+ * structure viewers.
+ *
+ * @return
+ */
+ boolean isSimple();
+}