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oglycans first commit #16

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oglycans first commit #16

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4ab7b5f
Update download link to overview page with all versions
RalfG Apr 23, 2021
c8430de
Merge pull request #15 from compomics/update-readme
RalfG Apr 26, 2021
daf249c
oglycans first commit
nielshulstaert May 10, 2021
496bab4
oglycans first commit
nielshulstaert May 10, 2021
bbeb87f
second commit with latest utilities version
nielshulstaert May 10, 2021
c94f308
second commit with latest utilities version
nielshulstaert May 10, 2021
556806c
typo fix
nielshulstaert May 10, 2021
a26eb4f
typo fix
nielshulstaert May 10, 2021
077d02a
Merge branch 'master' of https://github.com/compomics/COSS
May 10, 2021
d65818e
Merge branch 'master' into glycan
nielshulstaert May 10, 2021
18c0596
Merge branch 'master' into glycan
nielshulstaert May 10, 2021
90592c7
fragmentation and spec generation added
May 10, 2021
66a9e7e
fragmentation and spec generation added
May 10, 2021
a84778a
corrections
May 10, 2021
bf596aa
corrections
May 10, 2021
50a05fa
fastareader changes
nielshulstaert May 10, 2021
bf2c89e
fastareader changes
nielshulstaert May 10, 2021
31b227c
modified
May 10, 2021
a7f738e
modified
May 10, 2021
a7738ca
modified2
May 10, 2021
c95224e
modified2
May 10, 2021
bc09fd1
fastareader changes
nielshulstaert May 10, 2021
7ee7495
fastareader changes
nielshulstaert May 10, 2021
5056c0f
m
May 10, 2021
6b61c95
prec. mass added
May 10, 2021
33eba81
Merge branch 'glycan' of https://github.com/compomics/COSS into glycan
May 10, 2021
d5b6f11
deleted
May 10, 2021
fd2fdbe
error
May 10, 2021
419ece9
error fixed
May 10, 2021
5351ff3
fastareader changes
nielshulstaert May 10, 2021
7058b2a
Merge branch 'glycan' of https://github.com/compomics/COSS into glycan
nielshulstaert May 25, 2021
e3cb71c
added fixed mod check to test
nielshulstaert May 25, 2021
15a0e25
modification updated
May 25, 2021
55587fc
modified
May 25, 2021
82801fe
error fixed
May 25, 2021
e3d212d
small fix
nielshulstaert May 25, 2021
8148391
Merge branch 'glycan' of https://github.com/compomics/COSS into glycan
nielshulstaert May 25, 2021
a622755
Conversion from utilities peptide to coss objects
nielshulstaert May 26, 2021
a113ab3
before merge problems
nielshulstaert May 26, 2021
2dc127c
Revert "small change made"
nielshulstaert May 26, 2021
caeb7fa
error fixed
May 27, 2021
803461c
commit before merge
nielshulstaert May 27, 2021
11dfe8a
commit before pull
nielshulstaert May 28, 2021
f9c06de
error solved
May 28, 2021
eda5853
Merge branch 'glycan' of https://github.com/compomics/COSS into glycan
nielshulstaert Jun 2, 2021
fd2382a
ongoing glycan changes
nielshulstaert Jun 24, 2021
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8 changes: 8 additions & 0 deletions .gitignore
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Expand Up @@ -8,3 +8,11 @@ dist/
nbdist/
nbactions.xml
nb-configuration.xml
test.msp

### JetBrains template
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
*.iml

## Directory-based project format:
.idea/
27 changes: 19 additions & 8 deletions pom.xml
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Expand Up @@ -40,8 +40,8 @@
<version>2.5.1</version>
<inherited>true</inherited>
<configuration>
<source>1.8</source>
<target>1.8</target>
<source>8</source>
<target>8</target>
<showDeprecation>true</showDeprecation>
<debug>true</debug>
</configuration>
Expand Down Expand Up @@ -193,24 +193,29 @@
<layout>default</layout>
</repository>

<repository>
<!-- <repository>
<id>netbeans</id>
<name>Netbeans rep</name>
<url>http://bits.netbeans.org/maven2/</url>
</repository>
</repository>-->

<repository>
<id>netbeans</id>
<name>NetBeans</name>
<url>http://netbeans.apidesign.org/maven2/</url>
</repository>

<!-- <repository>
<id>unknown-jars-temp-repo</id>
<name>A temporary repository created by NetBeans for libraries and jars it could not identify. Please replace the dependencies in this repository with correct ones and delete this repository.</name>
<url>file:${project.basedir}/lib</url>
</repository>
</repository>-->

<!-- JPL library repository-->
<repository>
<id>Expasy MzJava</id>
<url>http://mzjava.expasy.org/maven</url>
</repository>

</repository>

<!-- EBI jmzReader -->
<repository>
Expand Down Expand Up @@ -240,7 +245,7 @@
<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>4.11.18</version>
<version>5.0.9</version>
<exclusions>
<exclusion>
<artifactId>commons-math</artifactId>
Expand Down Expand Up @@ -376,6 +381,12 @@
<groupId>com.compomics</groupId>
<artifactId>MS2IO</artifactId>
<version>1.1</version>
<!-- <exclusions>-->
<!-- <exclusion>-->
<!-- <groupId>com.compomics</groupId>-->
<!-- <artifactId>utilities</artifactId>-->
<!-- </exclusion>-->
<!-- </exclusions>-->
</dependency>

<dependency>
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/com/compomics/coss/controller/featureExtraction/DivideAndTopNPeaks.java
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Expand Up @@ -14,7 +14,8 @@
public class DivideAndTopNPeaks implements Features {

// private int topN;
private int windowMassSize = 100;
private int windowMassSize = 10;
// private int windowMassSize = 100;
private final Logger LOGGER;
// ArrayList<Peak> cPeaks;
// ArrayList<Peak> filteredPeaks;
Expand Down
7 changes: 6 additions & 1 deletion src/main/java/com/compomics/coss/controller/matching/CosineSimilarity.java
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Expand Up @@ -61,11 +61,14 @@ public double calculateScore(ArrayList<Peak> expSpec, ArrayList<Peak> libSpec, i
double intScore=-1;
try{
intScore=cosineScore(mPeaksExp, mPeaksLib);// * (mPeaksExp.size()/(double)lenA);

}catch(ArithmeticException ex){
System.out.println(ex.toString());
}

double finalScore=intScore*matchedNumPeaks;

//double finalScore=intScore*matchedNumPeaks;
double finalScore= matchedNumPeaks; //removed intscore for glycan
return finalScore;
}

Expand All @@ -90,4 +93,6 @@ private double cosineScore(List<Peak> v1, List<Peak> v2) { // parameters vector1
return score;
}



}
3 changes: 2 additions & 1 deletion src/main/java/com/compomics/coss/controller/matching/DataProducer.java
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Expand Up @@ -96,7 +96,8 @@ public void run() {
expSpec = confData.getExpSpecReader().readAt(confData.getExpSpectraIndex().get(a).getPos());
double mass = expSpec.getPCMass();

double da_error = mass * this.precTolerance;
//double da_error = mass * this.precTolerance;
double da_error = this.precTolerance;

libSpec = confData.getLibSpecReader().readPart(mass, da_error);
// synchronized (data) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/com/compomics/coss/controller/matching/MSRobin.java
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Expand Up @@ -67,7 +67,7 @@ public double calculateScore(ArrayList<Peak> expSpec, ArrayList<Peak> libSpec, i
sumMatchedIntExp = getSumIntensity(mPeaksExp);
sumMatchedIntLib = getSumIntensity(mPeaksLib);

intensity_part = calculateIntensityPart(mPeaksExp, mPeaksLib);
intensity_part = 1;// calculateIntensityPart(mPeaksExp, mPeaksLib);

//finalScore = intensity_part * calculateJaccard(matchedNumPeaks, lenA, lenB);
finalScore = getfinalScore(totalN, probability, intensity_part);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/com/compomics/coss/controller/matching/MatchedPeaks.java
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Expand Up @@ -64,7 +64,8 @@ public Map getMatchedPeaks(ArrayList<Peak> filteredExpMS2_1, ArrayList<Peak> fil
for (int i = 0; i < filteredExpMS2_1.size(); i++) {
Peak p1 = filteredExpMS2_1.get(i);
double mz_p1 = p1.getMz();
double diff = fragTolerance;// Based on Da.. not ppm...
// double diff = fragTolerance;// Based on Da.. not ppm...
double diff = mz_p1 * fragTolerance;// Based on PPM!
boolean found = false;
Peak matchedPeak_2 = null;
for (Peak peak_expMS2_2 : filteredExpMS2_2) {
Expand Down
10 changes: 4 additions & 6 deletions src/main/java/com/compomics/coss/view/MainFrame.form
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Expand Up @@ -137,7 +137,6 @@
</NonVisualComponents>
<Properties>
<Property name="defaultCloseOperation" type="int" value="3"/>
<Property name="resizable" type="boolean" value="false"/>
<Property name="size" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
<Dimension value="[700, 700]"/>
</Property>
Expand Down Expand Up @@ -255,7 +254,7 @@
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" attributes="0">
<Group type="103" groupAlignment="0" attributes="0">
<Component id="jPanel7" pref="627" max="32767" attributes="0"/>
<Component id="jPanel7" pref="629" max="32767" attributes="0"/>
<Group type="102" attributes="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" attributes="0">
Expand Down Expand Up @@ -348,7 +347,6 @@
<Component id="txtfragTolerance" min="-2" pref="49" max="-2" attributes="0"/>
<EmptySpace type="separate" max="-2" attributes="0"/>
<Component id="cmbfragmentTolerance" min="-2" max="-2" attributes="0"/>
<EmptySpace max="32767" attributes="0"/>
</Group>
<Group type="102" alignment="0" attributes="0">
<Component id="txtprecTolerance" min="-2" pref="49" max="-2" attributes="0"/>
Expand All @@ -366,7 +364,7 @@
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="0" attributes="0">
<EmptySpace pref="14" max="32767" attributes="0"/>
<EmptySpace max="32767" attributes="0"/>
<Group type="103" groupAlignment="3" attributes="0">
<Component id="jLabel1" alignment="3" min="-2" max="-2" attributes="0"/>
<Component id="txtqueryspec" alignment="3" min="-2" max="-2" attributes="0"/>
Expand Down Expand Up @@ -1095,7 +1093,7 @@
</Group>
</Group>
</Group>
<Component id="pnlQuerySpecViz" alignment="0" pref="529" max="32767" attributes="0"/>
<Component id="pnlQuerySpecViz" alignment="0" pref="511" max="32767" attributes="0"/>
</Group>
</DimensionLayout>
<DimensionLayout dim="1">
Expand Down Expand Up @@ -1260,7 +1258,7 @@
</DimensionLayout>
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<EmptySpace min="0" pref="199" max="32767" attributes="0"/>
<EmptySpace min="0" pref="181" max="32767" attributes="0"/>
</Group>
</DimensionLayout>
</Layout>
Expand Down
14 changes: 6 additions & 8 deletions src/main/java/com/compomics/coss/view/MainFrame.java
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Expand Up @@ -127,7 +127,6 @@ private void initComponents() {
jMenu4 = new javax.swing.JMenu();

setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
setResizable(false);
setSize(new java.awt.Dimension(700, 700));

spltPannelBase.setDividerLocation(650);
Expand Down Expand Up @@ -207,8 +206,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
.addGroup(jPanel7Layout.createSequentialGroup()
.addComponent(txtfragTolerance, javax.swing.GroupLayout.PREFERRED_SIZE, 49, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(cmbfragmentTolerance, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addComponent(cmbfragmentTolerance, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(jPanel7Layout.createSequentialGroup()
.addComponent(txtprecTolerance, javax.swing.GroupLayout.PREFERRED_SIZE, 49, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
Expand All @@ -219,7 +217,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
jPanel7Layout.setVerticalGroup(
jPanel7Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(jPanel7Layout.createSequentialGroup()
.addContainerGap(14, Short.MAX_VALUE)
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(jPanel7Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel1)
.addComponent(txtqueryspec, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
Expand Down Expand Up @@ -369,7 +367,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
jLayeredPane1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(jLayeredPane1Layout.createSequentialGroup()
.addGroup(jLayeredPane1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jPanel7, javax.swing.GroupLayout.DEFAULT_SIZE, 627, Short.MAX_VALUE)
.addComponent(jPanel7, javax.swing.GroupLayout.PREFERRED_SIZE, 629, Short.MAX_VALUE)
.addGroup(jLayeredPane1Layout.createSequentialGroup()
.addGroup(jLayeredPane1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(jLayeredPane1Layout.createSequentialGroup()
Expand Down Expand Up @@ -460,7 +458,7 @@ public void mouseClicked(java.awt.event.MouseEvent evt) {
);
jPanel15Layout.setVerticalGroup(
jPanel15Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jScrollPane4, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 24, Short.MAX_VALUE)
.addComponent(jScrollPane4, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, 24, Short.MAX_VALUE)
);

jSplitPane9.setTopComponent(jPanel15);
Expand Down Expand Up @@ -646,7 +644,7 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
);
pnlQuerySpecVizLayout.setVerticalGroup(
pnlQuerySpecVizLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGap(0, 199, Short.MAX_VALUE)
.addGap(0, 181, Short.MAX_VALUE)
);

javax.swing.GroupLayout jPanel3Layout = new javax.swing.GroupLayout(jPanel3);
Expand Down Expand Up @@ -682,7 +680,7 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(txtTotalSpec, javax.swing.GroupLayout.PREFERRED_SIZE, 56, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(0, 0, Short.MAX_VALUE))))
.addComponent(pnlQuerySpecViz, javax.swing.GroupLayout.DEFAULT_SIZE, 529, Short.MAX_VALUE)
.addComponent(pnlQuerySpecViz, javax.swing.GroupLayout.DEFAULT_SIZE, 511, Short.MAX_VALUE)
);
jPanel3Layout.setVerticalGroup(
jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
Expand Down
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