* @param type
* AlignSeq.DNA or AlignSeq.PEP
*/
+ //&! 1 v 1 needleman
public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
String type)
{
--- /dev/null
+/*
+ * 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.analysis;
+
+//import jalview.datamodel.AlignmentView;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.util.Hashtable;
+
+/**
+ * @Author MorellThomas
+ */
+
+public class Connectivity
+{
+
+ /**
+ * Returns the number of unique connections for each sequence
+ * only connections with a score of above 0 count
+ *
+ * @param av sequences
+ * @param scores alignment scores
+ *
+ * @return connectivity
+ */
+ public static Hashtable<SequenceI, Integer> getConnectivity(AlignmentViewport av, float[][] scores, byte dim) throws RuntimeException
+ {
+ SequenceI[] sequences = av.getAlignment().getSequencesArray();
+
+ Hashtable<SequenceI, Integer> connectivity = new Hashtable<SequenceI, Integer>();
+ // for each unique connection
+ for (int i = 0; i < sequences.length; i++)
+ {
+ connectivity.putIfAbsent(sequences[i], 0);
+ for (int j = 0; j < i; j++)
+ {
+ connectivity.putIfAbsent(sequences[j], 0);
+ int iOld = connectivity.get(sequences[i]);
+ int jOld = connectivity.get(sequences[j]);
+ // count the connection if its score is bigger than 0.1
+ if (scores[i][j] >= 0.1) // what is cutoff instead of just 0.1?
+ {
+ connectivity.put(sequences[i], ++iOld);
+ connectivity.put(sequences[j], ++jOld);
+ }
+ }
+ }
+ //Debug
+ for (int i = 0; i < sequences.length; i++)
+ {
+ System.out.println(connectivity.get(sequences[i]));
+ }
+
+ // if a sequence has too few connections, abort
+ connectivity.forEach((sequence, connection) ->
+ {
+ if (connection < dim)
+ {
+ // a popup saying that it failed would be nice
+ throw new ConnectivityException(sequence.getName(), connection, dim);
+ }
+ } );
+
+ return connectivity;
+ }
+
+}
--- /dev/null
+/*
+ * 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.analysis;
+
+public class ConnectivityException extends RuntimeException
+{
+ private String sequence;
+ private int connection;
+ private byte dim;
+
+ public ConnectivityException(String sequence, int connection, byte dim)
+ {
+ this("Insufficient number of connections", sequence, connection, dim);
+ }
+
+ public ConnectivityException(String message, String sequence, int connection, byte dim)
+ {
+ super(String.format("%s for %s (%d, should be %d or more)", message, sequence, connection, dim));
+ this.sequence = sequence;
+ this.connection = connection;
+ this.dim = dim;
+ }
+
+ public String getSequence()
+ {
+ return sequence;
+ }
+
+ public int getConnection()
+ {
+ return connection;
+ }
+
+ public byte getDim()
+ {
+ return dim;
+ }
+
+}
import jalview.bin.Console;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Point;
+import jalview.datamodel.SequenceI;
+import jalview.gui.PairwiseAlignPanel;
+import jalview.gui.PaSiMapPanel;
import jalview.math.MatrixI;
+import jalview.viewmodel.AlignmentViewport;
+
import java.io.PrintStream;
+import java.util.Hashtable;
+import java.util.Enumeration;
/**
* Performs Principal Component Analysis on given sequences
+ * @AUTHOR MorellThomas
*/
public class PaSiMap implements Runnable
{
/*
* inputs
*/
- final private AlignmentView seqs;
+ final private AlignmentViewport seqs;
final private ScoreModelI scoreModel;
final private SimilarityParamsI similarityParams;
+ final private byte dim = 3;
+
/*
* outputs
*/
* @param sm
* @param options
*/
- public PaSiMap(AlignmentView sequences, ScoreModelI sm,
+ //public PaSiMap(AlignmentView sequences, ScoreModelI sm,
+ //&! viewport or panel?
+ public PaSiMap(AlignmentViewport sequences, ScoreModelI sm,
SimilarityParamsI options)
{
this.seqs = sequences;
{
try
{
+ /** here goes pasimap
+ * FASTA_to_secureFASTA + sed s/ /_/g ~~ aliases = 1st word of secure fasta header
+ * FASTA_to_stats ~~ unique_headers_count, unique_bodies_count + check: unique_bodies_min, dim_max
+ * if unaligned : EMBOSS needlall ~~ alignments.fas
+ * elseif aligned : MSA_to_pairwiseFASTA
+ * pairwiseFASTA_to_pairwiseCSV
+ * pairwise_to_connectivity ~~ connectivity.csv + warn if sequence has #connections >= dim
+ * pairwiseCSV_to_pairwiseQuantifier (use scoreModel) + label results
+ * cc_analysis quantifier.ssv ~~ vec.ssv + label results
+ * plot
+ *
+ * ######################
+ *
+ * input AlignemtView seqs ~~ check if aligned
+ * if not ~~ perform needlall (or try whatever is in there)
+ * calculate connectivity + check if fine
+ * quantify alignment with ScoreModelI scoreModel
+ * cc_analysis with quantification
+ * plot whatever comes out of cc_analysis
+ */
+
+ /*
+ bool aligned = seqs.checkoridk;
+ if (!aligned)
+ {
+ seqs = needlall(seqs);
+ }
+
+ connectivity
+
+ pairwiseScores = scoreModel.findSimilarities(seqs, similarityParams);
+
+ cc_analysis
+ */
+
+ // run needleman regardless if aligned or not
+ // gui.PairwiseAlignPanel <++>
+ PairwiseAlignPanel alignment = new PairwiseAlignPanel(seqs);
+ float[][] scores = alignment.getScores();
+ System.out.println(scores[8][18]); // do scores have to be divided by totscore??
+
+ // what is connectivity and why?
+ Hashtable<SequenceI, Integer> connectivity = seqs.calculateConnectivity(scores, dim);
+
+
+ /** pca code */
/*
* sequence pairwise similarity scores
*/
- pairwiseScores = scoreModel.findSimilarities(seqs, similarityParams);
+ //&! analysis/scoremodels/ScoreMatrix computeSimilarity
+ //pairwiseScores = scoreModel.findSimilarities(seqs, similarityParams);
/*
* tridiagonal matrix
*/
- tridiagonal = pairwiseScores.copy();
- tridiagonal.tred();
+ //tridiagonal = pairwiseScores.copy();
+ //tridiagonal.tred();
/*
* the diagonalization matrix
*/
- eigenMatrix = tridiagonal.copy();
- eigenMatrix.tqli();
+ //eigenMatrix = tridiagonal.copy();
+ //eigenMatrix.tqli();
} catch (Exception q)
{
Console.error("Error computing PaSiMap: " + q.getMessage());
}
}
}
+ //&!
AlignmentI visal = view.getVisibleAlignment('-');
if (visal != null)
{
import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Color;
/*
* construct the panel and kick off its calculation thread
*/
- //&! change to PaSiMapPanel
pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName, params);
new Thread(pasimapPanel).start();
boolean selected = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 0;
+ //&! do i need seqstrings?
AlignmentView seqstrings = av.getAlignmentView(selected);
SequenceI[] seqs;
if (!selected)
ScoreModelI scoreModel = ScoreModels.getInstance()
.getScoreModel(modelName, ap);
setPasimapModel(
- new PaSiMapModel(seqstrings, seqs, nucleotide, scoreModel, params));
+ //&!
+ //new PaSiMapModel(seqstrings, seqs, nucleotide, scoreModel, params));
+ new PaSiMapModel(av, seqs, nucleotide, scoreModel, params));
PaintRefresher.Register(this, av.getSequenceSetId());
setRotatableCanvas(new RotatableCanvas(alignPanel));
}
Object[] alAndColsel = getPasimapModel().getInputData()
- .getAlignmentAndHiddenColumns(gc);
+ .getAlignmentView(false).getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
*
* @param data
*/
- public void setInputData(AlignmentView data)
+ //public void setInputData(AlignmentView data)
+ //&! viewport or panel?
+ public void setInputData(AlignmentViewport data)
{
getPasimapModel().setInputData(data);
originalSeqData.setVisible(data != null);
private static final String DASHES = "---------------------\n";
+ private float[][] scores;
+
AlignmentViewport av;
Vector<SequenceI> sequences;
}
}
+ this.scores = scores;
+
if (count > 2)
{
printScoreMatrix(seqs, scores, totscore);
}
}
+ public float[][] getScores()
+ {
+ return this.scores;
+ }
+
/**
* Prints a matrix of seqi-seqj pairwise alignment scores to sysout
*
package jalview.viewmodel;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.Connectivity;
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignCalcManagerI;
return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
false));
}
+
+ public Hashtable<SequenceI, Integer> calculateConnectivity(float[][] scores, byte dim)
+ {
+ return Connectivity.getConnectivity(this, scores, dim);
+ }
}
import jalview.datamodel.Point;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
+import jalview.viewmodel.AlignmentViewport;
import java.util.List;
import java.util.Vector;
/*
* inputs
*/
- private AlignmentView inputData;
+ //private AlignmentView inputData;
+ //&!
+ private AlignmentViewport inputData;
private final SequenceI[] seqs;
* @param modelName
* @param params
*/
- public PaSiMapModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ //public PaSiMapModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ //&! viewport or panel?
+ public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
ScoreModelI modelName, SimilarityParamsI params)
{
inputData = seqData;
return pasimap.getDetails();
}
- public AlignmentView getInputData()
+ //&!
+ //public AlignmentView getInputData()
+ public AlignmentViewport getInputData()
{
return inputData;
}
- public void setInputData(AlignmentView data)
+ //&!
+ //public void setInputData(AlignmentView data)
+ public void setInputData(AlignmentViewport data)
{
inputData = data;
}
git://source.jalview.org / jalview.git / commitdiff