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allows for offset in SA tree
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@jugne
jugne committed Sep 25, 2023
1 parent 98bc6b4 commit 712f7de
Showing 1 changed file with 52 additions and 13 deletions.
65 changes: 52 additions & 13 deletions src/sr/util/loggers/SRangesAndSACladeSetComparator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,7 @@
import java.awt.Graphics2D;
import java.awt.geom.AffineTransform;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.io.*;
import java.text.DecimalFormat;
import java.util.*;

Expand All @@ -35,6 +33,7 @@
+ "they can be plotted in an X-Y plot")
public class SRangesAndSACladeSetComparator extends Runnable {
final public Input<TreeFile> src1Input = new Input<>("SATree","source SA tree (set or MCC tree) file");
final public Input<TreeFile> SATreeOffsetInput = new Input<>("SALog","SA log file containing offset for each tree in SATree");
final public Input<TreeFile> src2Input = new Input<>("sRangesTree","source sRanges tree (set or MCC tree) file");

public Input<String> sepStringInput = new Input<>("sep",
Expand Down Expand Up @@ -127,8 +126,6 @@ public void initAndValidate() {


double maxHeight = 0.0;

double maxHeight2 = 0.0;
int problemCount = 0;
int interestCount = 0;
int inconsistentHeightIntervals = 0;
Expand Down Expand Up @@ -165,7 +162,6 @@ public void run() throws Exception {
CladeSetWithHeights cladeSet2 = getCladeSet(src2Input.get().getPath(), true);
double n2 = n;
process(src1Input.get(), src2Input.get(), "", cladeSet1, n1, cladeSet2, n2);
System.out.println("maxHeight2 = " + maxHeight2);
}

void process(TreeFile tree1, TreeFile tree2, String suffix,
Expand Down Expand Up @@ -462,8 +458,6 @@ private void output(PrintStream out, PrintStream svg, String clade, Double suppo
if (!compareOnly.containsAll(cladeList)){
return;
}
maxHeight2 = Double.max(maxHeight2, max2);
maxHeight2 = Double.max(maxHeight2, max1);
}
if (verbose || System.out != out) {
out.println(clade.replaceAll(" ", "") + " " + support1 + " " + support2 + " " + h1 +
Expand Down Expand Up @@ -543,6 +537,33 @@ private void output(PrintStream out, PrintStream svg, String clade, Double suppo
private CladeSetWithHeights getCladeSet(String path, boolean rangesTree) throws IOException {
Log.warning("Processing " + path);
MemoryFriendlyTreeSet srcTreeSet = new MemoryFriendlyTreeSet(path, burnInPercentageInput.get());
BufferedReader offsetFile = null;
int offsetIndex = 0;
if (!rangesTree && SATreeOffsetInput.get()!=null){
offsetFile = new BufferedReader(new FileReader(SATreeOffsetInput.get()));
String line = offsetFile.readLine();
int n = -1;
while(line != null && !line.startsWith("#")){
n+=1;
line = offsetFile.readLine();
}
offsetFile = new BufferedReader(new FileReader(SATreeOffsetInput.get()));
line = offsetFile.readLine();
while(line.startsWith("#"))
line = offsetFile.readLine();
String[] params = line.split("\t");
offsetIndex = findIndexOf(params, "offset");
for (int i=0; i<Math.max(0, (burnInPercentageInput.get() * n)/100); i++){
line = offsetFile.readLine();
}
line = offsetFile.readLine();
params = line.split("\t");
offset = Double.parseDouble(params[offsetIndex]);
}
else {
offset =0.;
}

srcTreeSet.reset();
Tree tree = srcTreeSet.next();
CladeSetWithHeights cladeSet1 = new CladeSetWithHeights(tree, rangesTree);
Expand All @@ -554,6 +575,13 @@ private CladeSetWithHeights getCladeSet(String path, boolean rangesTree) throws

while (srcTreeSet.hasNext()) {
// System.out.println(n);
if (!rangesTree && SATreeOffsetInput.get()!=null){
String line = offsetFile.readLine();
String[] params = line.split("\t");
offset = Double.parseDouble(params[offsetIndex]);
} else{
offset = 0.;
}
tree = srcTreeSet.next();
cladeSet1.add(tree, rangesTree);
n++;
Expand Down Expand Up @@ -627,8 +655,8 @@ void addClades(Node node, BitSet bits) {
}

void addNodeHeight(BitSet bits, double height, double lo, double hi) {
totalNodeHeight.put(bits, (getTotalNodeHeight(bits) + height));
nodeHeights.put(bits, new double[]{lo, height, hi});
totalNodeHeight.put(bits, (getTotalNodeHeight(bits) + (height+offset)));
nodeHeights.put(bits, new double[]{lo+offset, height+offset, hi+offset});
}

Map<BitSet, Double> posteriors = new HashMap<>();
Expand Down Expand Up @@ -790,12 +818,12 @@ public double getMaxNodeHeight(int i) {
private void addNodeHeight(BitSet bits, double height) {
totalNodeHeight.put(bits, (getTotalNodeHeight(bits) + height));
if (!nodeHeights.containsKey(bits)) {
nodeHeights.put(bits, new double[]{height});
nodeHeights.put(bits, new double[]{height+offset});
} else {
double [] heights = nodeHeights.get(bits);
double [] newHeights = new double[heights.length + 1];
System.arraycopy(heights, 0, newHeights, 0, heights.length);
newHeights[heights.length] = height;
newHeights[heights.length] = height+offset;
nodeHeights.put(bits, newHeights);
}
}
Expand Down Expand Up @@ -900,15 +928,26 @@ private int findClade(BitSet bitSet, Node node, Node[] cladeMRCA) {
Set<String> taxonNames = null;
Map<BitSet, Double> totalNodeHeight = new HashMap<>();
Map<BitSet, double[]> nodeHeights = new HashMap<>();

Set<BitSet> addedForThisTree = new HashSet<>();
int totalTrees = 0;
}


double offset = 0.;
public static void main(String[] args) throws Exception {
new Application(new SRangesAndSACladeSetComparator(), "Clade Set Comparator", args);

}

// Helper method to find the index of a specific value in an array
public static int findIndexOf(String[] array, String value) {
for (int i = 0; i < array.length; i++) {
if (array[i].equals(value)) {
return i;
}
}
return -1; // Value not found
}


}

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