From: kjvdheide Date: Sun, 29 Oct 2017 16:51:31 +0000 (+0000) Subject: JAL-2795 more matrix implementations X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b1e2aea95b3839a1a53f809c579666075cd3d348;p=jalview.git JAL-2795 more matrix implementations --- diff --git a/forester b/forester index d62c120..09a8c72 160000 --- a/forester +++ b/forester @@ -1 +1 @@ -Subproject commit d62c120f4c6fb10f20abaa929514d980fcea9671 +Subproject commit 09a8c723e9ab220999f25c6be635282f18186be7 diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java index 39106a7..d4864cf 100644 --- a/src/jalview/ext/forester/ForesterMatrix.java +++ b/src/jalview/ext/forester/ForesterMatrix.java @@ -1,21 +1,41 @@ package jalview.ext.forester; +import jalview.datamodel.Sequence; import jalview.math.MatrixI; +import java.io.IOException; +import java.io.Writer; +import java.text.DecimalFormat; +import java.text.NumberFormat; + import org.forester.evoinference.matrix.distance.DistanceMatrix; +import org.forester.util.ForesterUtil; +import org.forester.util.IllegalFormatUseException; public class ForesterMatrix implements DistanceMatrix { - private MatrixI jalviewMatrix; + private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat( + "0.000000"); // straight from forester + + private final MatrixI jalviewMatrix; + + private final Sequence[] sequences; - public ForesterMatrix(MatrixI jalviewInputMatrix) + private final double[][] values; + + public ForesterMatrix(MatrixI jalviewInputMatrix, + Sequence[] matrixSequences) { this.jalviewMatrix = jalviewInputMatrix; + this.sequences = matrixSequences; + if (jalviewMatrix.width() != jalviewMatrix.height()) { - + // some kind of warning? } + values = new double[jalviewMatrix.width()][jalviewMatrix.height()]; + } @Override @@ -67,8 +87,47 @@ public class ForesterMatrix implements DistanceMatrix @Override public double[][] getValues() { - // TODO Auto-generated method stub + return null; } + @Override + public void write(Writer w) throws IOException // directly copied from + // forester + { + w.write(" "); + w.write(getSize() + ""); + w.write(ForesterUtil.LINE_SEPARATOR); + for (int row = 0; row < getSize(); ++row) + { + if (!ForesterUtil.isEmpty(getIdentifier(row))) + { + w.write(ForesterUtil.pad(getIdentifier(row), 10, ' ', false) + .toString()); + w.write(' '); + w.write(' '); + } + else + { + throw new IllegalFormatUseException( + "Phylip format does not allow empty identifiers"); + } + for (int col = 0; col < getSize(); ++col) + { + w.write(PHYLIP_FORMATTER.format(getValue(col, row))); + if (col < (getSize() - 1)) + { + w.write(' '); + w.write(' '); + } + } + if (row < (getSize() - 1)) + { + w.write(ForesterUtil.LINE_SEPARATOR); + } + } + + } + + } \ No newline at end of file