X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=0bf40960b357075a97f049efdffba08195418c5f;hb=4b3e12d9f3c2e2ad8a0317160881cef075690e97;hp=5caded1ec3053b177a61b686ef4c9d7edaad3812;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 5caded1..0bf4096 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,28 +1,25 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * 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
+ * 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 .
+ *
+ * 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.io.vamsas;
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.NJTree;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
@@ -32,10 +29,17 @@ import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignViewport;
import jalview.gui.TreePanel;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.Entry;
@@ -99,7 +103,7 @@ public class Tree extends DatastoreItem
/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#addFromDocument()
*/
@Override
@@ -130,7 +134,7 @@ public class Tree extends DatastoreItem
/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#conflict()
*/
@Override
@@ -142,7 +146,7 @@ public class Tree extends DatastoreItem
/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#update()
*/
@Override
@@ -163,7 +167,7 @@ public class Tree extends DatastoreItem
/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
*/
@Override
@@ -174,7 +178,7 @@ public class Tree extends DatastoreItem
// TODO: Tree.updateFromDoc
/*
* TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
- *
+ *
* // make a new tree Object[] idata =
* recoverInputData(tree.getProvenance()); try { if (idata != null &&
* idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
@@ -201,7 +205,7 @@ public class Tree extends DatastoreItem
/**
* correctly creates provenance for trees calculated on an alignment by
* jalview.
- *
+ *
* @param jal
* @param tp
* @return
@@ -256,7 +260,7 @@ public class Tree extends DatastoreItem
/**
* look up SeqCigars in an existing alignment.
- *
+ *
* @param jal
* @param sequences
* @return vector of alignment sequences in order of SeqCigar array (but
@@ -268,22 +272,24 @@ public class Tree extends DatastoreItem
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
Vector alsq = new Vector();
List jalsqs;
- synchronized (jalsqs=jal.getSequences())
- {for (SequenceI asq:jalsqs)
+ synchronized (jalsqs = jal.getSequences())
{
- for (int t = 0; t < sequences.length; t++)
+ for (SequenceI asq : jalsqs)
{
- if (tseqs[t] != null
- && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
- .getDatasetSequence()))
- // && tseqs[t].getStart()>=asq.getStart() &&
- // tseqs[t].getEnd()<=asq.getEnd())
+ for (int t = 0; t < sequences.length; t++)
{
- tseqs[t] = null;
- alsq.add(asq);
+ if (tseqs[t] != null
+ && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
+ .getDatasetSequence()))
+ // && tseqs[t].getStart()>=asq.getStart() &&
+ // tseqs[t].getEnd()<=asq.getEnd())
+ {
+ tseqs[t] = null;
+ alsq.add(asq);
+ }
}
}
- }}
+ }
if (alsq.size() < sequences.length)
Cache.log
.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
@@ -291,9 +297,9 @@ public class Tree extends DatastoreItem
}
/**
- *
+ *
* Update jalview newick representation with TreeNode map
- *
+ *
* @param tp
* the treepanel that this tree is bound to.
*/
@@ -358,7 +364,7 @@ public class Tree extends DatastoreItem
// / TODO: refactor to vamsas :start
/**
* construct treenode mappings for mapped sequences
- *
+ *
* @param ntree
* @param newick
* @return
@@ -416,8 +422,7 @@ public class Tree extends DatastoreItem
tnv.copyInto(tn);
return tn;
}
- return new Treenode[]
- {};
+ return new Treenode[] {};
}
private String makeNodeSpec(Hashtable nodespecs,
@@ -435,7 +440,7 @@ public class Tree extends DatastoreItem
/**
* call to match up Treenode specs to NJTree parsed from document object.
- *
+ *
* @param nodespec
* @param leaves
* as returned from NJTree.findLeaves( .., ..) ..
@@ -476,7 +481,7 @@ public class Tree extends DatastoreItem
// todo: end refactor to vamsas library
/**
* add jalview object to vamsas document
- *
+ *
*/
@Override
public void addToDocument()
@@ -497,7 +502,7 @@ public class Tree extends DatastoreItem
/**
* note: this function assumes that all sequence and alignment objects
* referenced in input data has already been associated with jalview objects.
- *
+ *
* @param tp
* @param alignFrame
* @return Object[] { AlignmentView, AlignmentI - reference alignment for
@@ -505,7 +510,7 @@ public class Tree extends DatastoreItem
*/
public Object[] recoverInputData(Provenance tp)
{
- AlignViewport javport = null;
+ AlignmentViewport javport = null;
jalview.datamodel.AlignmentI jal = null;
jalview.datamodel.CigarArray view = null;
for (int pe = 0; pe < tp.getEntryCount(); pe++)
@@ -590,8 +595,7 @@ public class Tree extends DatastoreItem
// off by
// one for to
}
- return new Object[]
- { new AlignmentView(view), jal };
+ return new Object[] { new AlignmentView(view), jal };
}
}
Cache.log
@@ -599,7 +603,7 @@ public class Tree extends DatastoreItem
return null;
}
- private AlignViewport getViewport(Vobject v_parent)
+ private AlignmentViewport getViewport(Vobject v_parent)
{
if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
{