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New Peptide decoy generation options for Peptide utility module
Two dimensional q-value calculation for fragments Bump to 3.0.0
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32 changes: 32 additions & 0 deletions
32
src/edu/umich/andykong/ptmshepherd/core/AAMutationRules.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| package edu.umich.andykong.ptmshepherd.core; | ||
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| import java.util.HashMap; | ||
| import java.util.Map; | ||
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| public class AAMutationRules { | ||
| public static Map<Character, Character> mutateFrom = new HashMap<>(); | ||
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| // These rules are taken from DIA-NN | ||
| static { | ||
| mutateFrom.put('G', 'L'); | ||
| mutateFrom.put('A', 'L'); | ||
| mutateFrom.put('V', 'L'); | ||
| mutateFrom.put('L', 'V'); | ||
| mutateFrom.put('I', 'V'); | ||
| mutateFrom.put('F', 'L'); | ||
| mutateFrom.put('M', 'L'); | ||
| mutateFrom.put('P', 'L'); | ||
| mutateFrom.put('W', 'L'); | ||
| mutateFrom.put('S', 'T'); | ||
| mutateFrom.put('C', 'S'); | ||
| mutateFrom.put('T', 'S'); | ||
| mutateFrom.put('Y', 'S'); | ||
| mutateFrom.put('H', 'S'); | ||
| mutateFrom.put('K', 'L'); | ||
| mutateFrom.put('R', 'L'); | ||
| mutateFrom.put('Q', 'N'); | ||
| mutateFrom.put('E', 'D'); | ||
| mutateFrom.put('N', 'Q'); | ||
| mutateFrom.put('D', 'E'); | ||
| } | ||
| } |
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96 changes: 96 additions & 0 deletions
96
src/edu/umich/andykong/ptmshepherd/iterativelocalization/TwoDimJointCMF.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| package edu.umich.andykong.ptmshepherd.iterativelocalization; | ||
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| public class TwoDimJointCMF { | ||
| double probGrid[][]; | ||
| int countGrid[][]; | ||
| int nVals; | ||
| TwoDimJointPMF PMF; | ||
| boolean direction1; | ||
| boolean direction2; | ||
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| public TwoDimJointCMF(TwoDimJointPMF PMF, boolean direction1, boolean direction2) { | ||
| this.probGrid = new double[PMF.getXDim()][PMF.getYDim()]; | ||
| this.countGrid = new int[PMF.getXDim()][PMF.getYDim()]; | ||
| this.PMF = PMF; | ||
| this.nVals = PMF.nVals; | ||
| this.direction1 = direction1; | ||
| this.direction2 = direction2; | ||
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| calculateCMF(); | ||
| } | ||
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| private void calculateCMF() { | ||
| // First two loops are to calculate this for every value | ||
| for (int i1 = 0; i1 < getXDim(); i1++) { | ||
| for (int j1 = 0; j1 < getYDim(); j1++) { | ||
| int count = 0; // Number of vals to be integrated | ||
| // These two loops are the values that will be integrated | ||
| for (int i2 = 0; i2 <= i1; i2++) { // Sum values up to X (intensity) | ||
| for (int j2 = j1; j2 >= 0; j2--) { // Sum values great than Y (mass error) | ||
| count++; | ||
| } | ||
| } | ||
| this.countGrid[i1][j1] = count; | ||
| this.probGrid[i1][j1] = (double) count / (double) this.nVals; | ||
| } | ||
| } | ||
| } | ||
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| public int getXDim() { | ||
| return this.countGrid.length; | ||
| } | ||
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| public int getYDim() { | ||
| return this.countGrid[0].length; | ||
| } | ||
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| public String toString() { | ||
| StringBuffer sb = new StringBuffer(); | ||
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| sb.append("count grid"); | ||
| for (int j = 0; j < getXDim(); j++) { | ||
| sb.append(j + ".\t"); | ||
| } | ||
| sb.append("\n"); | ||
| for (int i = 0; i < getYDim(); i++) { | ||
| sb.append(i + ".\t"); | ||
| for (int j = 0; j < getXDim(); j++) | ||
| sb.append(String.format("%d\t", this.countGrid[j][i])); | ||
| sb.append("\n"); | ||
| } | ||
| sb.append("\t"); | ||
| sb.append("\n"); | ||
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| sb.append("prob grid\n"); | ||
| for (int i = 0; i < getYDim(); i++) { | ||
| sb.append(i + ".\t"); | ||
| for (int j = 0; j < getXDim(); j++) | ||
| sb.append(String.format("%.2f\t", this.probGrid[j][i])); | ||
| sb.append("\n"); | ||
| } | ||
| sb.append("\t"); | ||
| for (int j = 0; j < getXDim(); j++) { | ||
| sb.append(j + ".\t\t"); | ||
| } | ||
| sb.append("\n"); | ||
| return sb.toString(); | ||
| } | ||
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| public static void main(String args[]) { | ||
| TwoDimJointPMF tmpPMF = new TwoDimJointPMF(2,4,true,true); | ||
| tmpPMF.addVal(0, 0); | ||
| tmpPMF.addVal(0, 1); | ||
| tmpPMF.addVal(0, 2); | ||
| tmpPMF.addVal(0, 3); | ||
| tmpPMF.addVal(1, 0); | ||
| tmpPMF.addVal(1, 1); | ||
| tmpPMF.addVal(1, 2); | ||
| tmpPMF.addVal(1, 3); | ||
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| TwoDimJointCMF tmpCMF = new TwoDimJointCMF(tmpPMF, true, true); | ||
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| System.out.println(tmpCMF); | ||
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| } | ||
| } |
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