X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=cea1c5b29fc4ec56d6bae3708a5f6f491a792822;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=1d37fa67da7f2ea42c745ef38a64d857062d1f51;hpb=4956fb78f7222e84d0d7008a6b91146d6c61d151;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 1d37fa6..cea1c5b 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -5,16 +5,16 @@
* 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 License
+ * 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 License for more details.
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General License
+ * 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.
*/
@@ -31,23 +31,46 @@ import java.util.Set;
public interface AlignmentI extends AnnotatedCollectionI
{
/**
- * Calculates the number of sequences in an alignment
+ * Calculates the number of sequences in an alignment, excluding hidden
+ * sequences
*
* @return Number of sequences in alignment
*/
int getHeight();
/**
+ * Calculates the number of sequences in an alignment, including hidden
+ * sequences
*
- * Calculates the maximum width of the alignment, including gaps.
+ * @return Number of sequences in alignment
+ */
+ int getAbsoluteHeight();
+
+ /**
*
- * @return Greatest sequence length within alignment, or -1 if no sequences
- * present
+ * Answers the width of the alignment, including gaps, that is, the length of
+ * the longest sequence, or -1 if there are no sequences. Avoid calling this
+ * method repeatedly where possible, as it has to perform a calculation. Note
+ * that this width includes any hidden columns.
+ *
+ * @return
+ * @see AlignmentI#getVisibleWidth()
*/
@Override
int getWidth();
/**
+ *
+ * Answers the visible width of the alignment, including gaps, that is, the
+ * length of the longest sequence, excluding any hidden columns. Answers -1 if
+ * there are no sequences. Avoid calling this method repeatedly where
+ * possible, as it has to perform a calculation.
+ *
+ * @return
+ */
+ int getVisibleWidth();
+
+ /**
* Calculates if this set of sequences (visible and invisible) are all the
* same length
*
@@ -65,6 +88,15 @@ public interface AlignmentI extends AnnotatedCollectionI
boolean isAligned(boolean includeHidden);
/**
+ * Answers if the sequence at alignmentIndex is hidden
+ *
+ * @param alignmentIndex
+ * the index to check
+ * @return true if the sequence is hidden
+ */
+ boolean isHidden(int alignmentIndex);
+
+ /**
* Gets sequences as a Synchronized collection
*
* @return All sequences in alignment.
@@ -90,6 +122,17 @@ public interface AlignmentI extends AnnotatedCollectionI
SequenceI getSequenceAt(int i);
/**
+ * Find a specific sequence in this alignment.
+ *
+ * @param i
+ * Index of required sequence in full alignment, i.e. if all columns
+ * were visible
+ *
+ * @return SequenceI at given index.
+ */
+ SequenceI getSequenceAtAbsoluteIndex(int i);
+
+ /**
* Returns a map of lists of sequences keyed by sequence name.
*
* @return
@@ -118,7 +161,9 @@ public interface AlignmentI extends AnnotatedCollectionI
SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
- * Deletes a sequence from the alignment
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param s
* Sequence to be deleted.
@@ -126,7 +171,9 @@ public interface AlignmentI extends AnnotatedCollectionI
void deleteSequence(SequenceI s);
/**
- * Deletes a sequence from the alignment.
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param i
* Index of sequence to be deleted.
@@ -134,6 +181,14 @@ public interface AlignmentI extends AnnotatedCollectionI
void deleteSequence(int i);
/**
+ * Deletes a sequence in the alignment which has been hidden.
+ *
+ * @param i
+ * Index of sequence to be deleted
+ */
+ void deleteHiddenSequence(int i);
+
+ /**
* Finds sequence in alignment using sequence name as query.
*
* @param name
@@ -156,15 +211,17 @@ public interface AlignmentI extends AnnotatedCollectionI
int findIndex(SequenceI s);
/**
- * Finds group that given sequence is part of.
+ * Returns the first group (in the order in which groups were added) that
+ * includes the given sequence instance and aligned position (base 0), or null
+ * if none found
*
- * @param s
- * Sequence in alignment.
+ * @param seq
+ * - must be contained in the alignment (not a dataset sequence)
+ * @param position
*
- * @return First group found for sequence. WARNING : Sequences may be members
- * of several groups. This method is incomplete.
+ * @return
*/
- SequenceGroup findGroup(SequenceI s);
+ SequenceGroup findGroup(SequenceI seq, int position);
/**
* Finds all groups that a given sequence is part of.
@@ -284,13 +341,6 @@ public interface AlignmentI extends AnnotatedCollectionI
char getGapCharacter();
/**
- * Test for all nucleotide alignment
- *
- * @return true if alignment is nucleotide sequence
- */
- boolean isNucleotide();
-
- /**
* Test if alignment contains RNA structure
*
* @return true if RNA structure AligmnentAnnotation was added to alignment
@@ -298,12 +348,6 @@ public interface AlignmentI extends AnnotatedCollectionI
boolean hasRNAStructure();
/**
- * Set alignment to be a nucleotide sequence
- *
- */
- void setNucleotide(boolean b);
-
- /**
* Get the associated dataset for the alignment.
*
* @return Alignment containing dataset sequences or null of this is a
@@ -328,6 +372,8 @@ public interface AlignmentI extends AnnotatedCollectionI
HiddenSequences getHiddenSequences();
+ HiddenColumns getHiddenColumns();
+
/**
* Compact representation of alignment
*
@@ -426,7 +472,7 @@ public interface AlignmentI extends AnnotatedCollectionI
* @param results
* @return -1 or index of sequence in alignment
*/
- int findIndex(SearchResults results);
+ int findIndex(SearchResultsI results);
/**
* append sequences and annotation from another alignment object to this one.
@@ -472,8 +518,6 @@ public interface AlignmentI extends AnnotatedCollectionI
* - null or specific sequence reference
* @param groupRef
* - null or specific group reference
- * @param method
- * - CalcId for the annotation (must match)
*
* @return existing annotation matching the given attributes
*/
@@ -481,6 +525,17 @@ public interface AlignmentI extends AnnotatedCollectionI
boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
/**
+ * like findOrCreateAnnotation - looks for an existing alignment annotation
+ * row with matching name, calcId, sequenceRef, groupRef and autoCalculated
+ * flag and updates it from the annotation. If none is found the annotation is
+ * added directly.
+ *
+ * @param ala
+ * @return ala or the annotation row that was updated.
+ */
+ AlignmentAnnotation updateFromOrCopyAnnotation(AlignmentAnnotation ala);
+
+ /**
* move the given group up or down in the alignment by the given number of
* rows. Implementor assumes given group is already present on alignment - no
* recalculations are triggered.
@@ -549,11 +604,42 @@ public interface AlignmentI extends AnnotatedCollectionI
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
/**
- * Calculate the visible start and end index of an alignment. The result is
- * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+ * Set the hidden columns collection on the alignment. Answers true if the
+ * hidden column selection changed, else false.
*
- * @param hiddenCols
+ * @param cols
* @return
*/
- public int[] getVisibleStartAndEndIndex(List hiddenCols);
+ public boolean setHiddenColumns(HiddenColumns cols);
+
+ /**
+ * Insert a sequence at a position in an alignment
+ *
+ * @param i
+ * The index of the position.
+ * @param snew
+ * The new sequence.
+ */
+ void insertSequenceAt(int i, SequenceI snew);
+
+ /**
+ * Set the first sequence as representative and hide its insertions. Typically
+ * used when loading JPred files.
+ */
+ public void setupJPredAlignment();
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * sequence in al which sequences are aligned to
+ * @param input
+ * alignment view where sequence corresponding to profileseq is first
+ * entry
+ * @return new HiddenColumns for new alignment view, with insertions into
+ * profileseq marked as hidden.
+ */
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input);
}