From bcc737cf05d891b5c0693b42d4d9a90f5097f277 Mon Sep 17 00:00:00 2001
From: wenbostar <wenbostar@gmail.com>
Date: Sat, 30 Mar 2024 22:30:36 -0700
Subject: [PATCH] Fixed the following issues:
 https://github.com/wenbostar/PDV/issues/73
 https://github.com/wenbostar/PDV/issues/64

---
 pom.xml                                       | 30 +++++++++++++++----
 .../PDVGUI/gui/utils/GetPredictedOnline.java  | 23 +++++++++-----
 .../PDVGUI/gui/utils/SpectrumMainPanel.java   |  3 +-
 3 files changed, 42 insertions(+), 14 deletions(-)

diff --git a/pom.xml b/pom.xml
index 6421e0a..039db06 100644
--- a/pom.xml
+++ b/pom.xml
@@ -178,7 +178,7 @@
         <dependency>
             <groupId>com.github.chhh</groupId>
             <artifactId>msftbx</artifactId>
-            <version>1.8.2</version>
+            <version>1.8.8</version>
         </dependency>
 
         <dependency>
@@ -225,19 +225,29 @@
         <dependency>
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
-            <version>4.1.0</version>
+            <version>3.0.1</version>
         </dependency>
 
         <dependency>
             <groupId>uk.ac.ebi.pride.jaxb</groupId>
             <artifactId>pride-jaxb</artifactId>
-            <version>1.0.9</version>
+            <version>1.0.22</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>ch.qos.logback</groupId>
+                    <artifactId>logback-classic</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>ch.qos.logback</groupId>
+                    <artifactId>logback-core</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
         <dependency>
             <groupId>net.sf.jung</groupId>
             <artifactId>jung-visualization</artifactId>
-            <version>2.0.1</version>
+            <version>2.1.1</version>
         </dependency>
 
         <dependency>
@@ -255,7 +265,17 @@
         <dependency>
             <groupId>uk.ac.ebi.pride.utilities</groupId>
             <artifactId>pride-mod</artifactId>
-            <version>2.1.6</version>
+            <version>2.1.12</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>ch.qos.logback</groupId>
+                    <artifactId>logback-classic</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>ch.qos.logback</groupId>
+                    <artifactId>logback-core</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
         <dependency>
diff --git a/src/main/java/PDVGUI/gui/utils/GetPredictedOnline.java b/src/main/java/PDVGUI/gui/utils/GetPredictedOnline.java
index fac1b98..ba25fac 100644
--- a/src/main/java/PDVGUI/gui/utils/GetPredictedOnline.java
+++ b/src/main/java/PDVGUI/gui/utils/GetPredictedOnline.java
@@ -5,6 +5,7 @@
 import com.compomics.util.experiment.massspectrometry.MSnSpectrum;
 import com.compomics.util.experiment.massspectrometry.Peak;
 import com.compomics.util.experiment.massspectrometry.Precursor;
+import org.apache.commons.lang3.StringUtils;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.kohsuke.rngom.util.Uri;
@@ -13,6 +14,7 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.OutputStream;
+import java.math.BigDecimal;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.ProtocolException;
@@ -97,12 +99,19 @@ private void generateInputString(){
         } else {
             // Add the modifications to the peptide sequence
             // (the modifications are added in the order of their position in the peptide sequence)
-            int lastIndex = 0;
+            // pos: 1 - the first amino acid
+            String []aa_list = pepSeq.split("");
             for (int index : newMods.keySet()){
-                modPep += pepSeq.substring(lastIndex, index) + newMods.get(index);
-                lastIndex = index;
+                // TODO: C-term modification
+                if(index == 0){
+                    // N-term modification
+                    aa_list[0] = aa_list[0]+newMods.get(index);
+                }else{
+                    aa_list[index-1] = aa_list[index-1]+newMods.get(index);
+                }
             }
-            modPep += pepSeq.substring(lastIndex);
+            modPep = StringUtils.join(aa_list, "");
+            // System.out.println(modPep);
         }
 
         if (model.equals("AlphaPept_ms2_generic")){
@@ -206,9 +215,9 @@ public MSnSpectrum getSpectra() throws IOException {
 
                 HashMap<Double, Peak> peakHashMap = new HashMap<>();
                 for (int i = 0; i < intensity.size(); i++) {
-                    if ((double) intensity.get(i) > 0) {
-                        Peak peak = new Peak((double) mzs.get(i), (double) intensity.get(i));
-                        peakHashMap.put((double) mzs.get(i), peak);
+                    if (((BigDecimal) intensity.get(i)).doubleValue() > 0) {
+                        Peak peak = new Peak(((BigDecimal) mzs.get(i)).doubleValue(), ((BigDecimal) intensity.get(i)).doubleValue());
+                        peakHashMap.put(((BigDecimal) mzs.get(i)).doubleValue(), peak);
                     }
                 }
                 Charge charge = new Charge(1, precursorCharge);
diff --git a/src/main/java/PDVGUI/gui/utils/SpectrumMainPanel.java b/src/main/java/PDVGUI/gui/utils/SpectrumMainPanel.java
index 2f34b98..b447008 100644
--- a/src/main/java/PDVGUI/gui/utils/SpectrumMainPanel.java
+++ b/src/main/java/PDVGUI/gui/utils/SpectrumMainPanel.java
@@ -39,8 +39,6 @@
 import java.util.*;
 
 import static com.compomics.util.experiment.biology.Ion.IonType.*;
-import static com.compomics.util.experiment.biology.Ion.IonType.RELATED_ION;
-import static com.compomics.util.experiment.biology.Ion.IonType.REPORTER_ION;
 import static com.compomics.util.experiment.biology.NeutralLoss.H3PO4;
 
 /**
@@ -1680,6 +1678,7 @@ public void updateSpectrum(){
                     sequenceFragmentationPanel.setOpaque(false);
                     sequenceFragmentationPanel.setBackground(Color.WHITE);
 
+                    spectrumJLayeredPane.setLayer(spectrumPanel, JLayeredPane.DEFAULT_LAYER);
                     spectrumJLayeredPane.add(spectrumPanel);
 
                     spectrumPanel.setBounds(0, 75, spectrumShowPanel.getWidth(),spectrumShowPanel.getHeight()-85);