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Fixed predicted spectra import issues
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@KaiLiCn
KaiLiCn committed Jan 10, 2024
1 parent 68c052d commit 6a3c9ca
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Showing 5 changed files with 206 additions and 123 deletions.
5 changes: 4 additions & 1 deletion .idea/workspace.xml
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2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<groupId>PDV</groupId>
<artifactId>PDV</artifactId>
<packaging>jar</packaging>
<version>1.9.0</version>
<version>1.9.1</version>
<name>PDV</name>
<url>https://github.com/wenbostar/PDV</url>
<description>An integrative proteomics viewer</description>
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2 changes: 1 addition & 1 deletion src/main/java/PDVGUI/gui/PDVMainClass.java
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Original file line number Diff line number Diff line change
Expand Up @@ -262,7 +262,7 @@ public class PDVMainClass extends JFrame {
/**
* Version
*/
private static final String VERSION = "1.9.0";
private static final String VERSION = "1.9.1";

/**
* Main class
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251 changes: 139 additions & 112 deletions src/main/java/PDVGUI/gui/utils/GetPredictedOnline.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,22 +33,24 @@ public class GetPredictedOnline {
private HashMap<Integer, String> newMods;
private String inputString;
private double precursorMZ;
private String fragmentMethod;

public static void main(String[] args) throws IOException {

new GetPredictedOnline();
}

public GetPredictedOnline() throws IOException {
getSpectra();
getSpectra("");
}

public GetPredictedOnline(String model, String pepSeq, HashMap<Integer, String> newMods,
public GetPredictedOnline(String model, String pepSeq, HashMap<Integer, String> newMods, String fragmentMethod,
int precursorCharge, int collisionEnergy, String instrument, double precursorMZ) throws IOException {

this.model = model;
this.pepSeq = pepSeq;
this.newMods = newMods;
this.fragmentMethod = fragmentMethod;
this.precursorCharge = precursorCharge;
this.collisionEnergy = collisionEnergy;
this.instrument = instrument;
Expand Down Expand Up @@ -77,10 +79,12 @@ private void setURL() throws MalformedURLException {
} else if (model.equals("Prosit_2020_intensity_HCD")){
String url = "https://koina.proteomicsdb.org/v2/models/Prosit_2020_intensity_HCD/infer";
usedURL = new URL(url);
} else if (model.equals("Prosit_2023_intensity_XL_CMS2")){
String url = "https://koina.proteomicsdb.org/v2/models/Prosit_2023_intensity_XL_CMS2/infer";
usedURL = new URL(url);
} else if (model.equals("Prosit_2020_intensity_TMT")){
}
// else if (model.equals("Prosit_2023_intensity_XL_CMS2")){
// String url = "https://koina.proteomicsdb.org/v2/models/Prosit_2023_intensity_XL_CMS2/infer";
// usedURL = new URL(url);
// }
else if (model.equals("Prosit_2020_intensity_TMT")){
String url = "https://koina.proteomicsdb.org/v2/models/Prosit_2020_intensity_TMT/infer";
usedURL = new URL(url);
}
Expand All @@ -96,6 +100,7 @@ private void generateInputString(){
int lastIndex = 0;
for (int index : newMods.keySet()){
modPep += pepSeq.substring(lastIndex, index) + newMods.get(index);
lastIndex = index;
}
modPep += pepSeq.substring(lastIndex);
}
Expand Down Expand Up @@ -134,18 +139,22 @@ private void generateInputString(){
"\"shape\": [ 1, 1 ], \"datatype\": \"INT32\", \"data\": [ "+ precursorCharge + " ] }, { \"name\": " +
"\"collision_energies\", \"shape\": [ 1, 1 ], \"datatype\": \"FP32\", \"data\": [ "+ collisionEnergy +
" ] }] }";
} else if (model.equals("Prosit_2023_intensity_XL_CMS2")){
inputString = "{ \"id\": \"0\", \"inputs\": [ { \"name\": \"peptide_sequences\", \"shape\": [ 1, 1 ], " +
"\"datatype\": \"BYTES\", \"data\": [ \"" + modPep + "\" ] }, { \"name\": \"precursor_charges\", " +
"\"shape\": [ 1, 1 ], \"datatype\": \"INT32\", \"data\": [ "+ precursorCharge + " ] }, { \"name\": " +
"\"collision_energies\", \"shape\": [ 1, 1 ], \"datatype\": \"FP32\", \"data\": [ "+ collisionEnergy +
" ] }] }";
} else if (model.equals("Prosit_2020_intensity_TMT")){
}
// else if (model.equals("Prosit_2023_intensity_XL_CMS2")){
// inputString = "{ \"id\": \"0\", \"inputs\": [ { \"name\": \"peptide_sequences\", \"shape\": [ 1, 1 ], " +
// "\"datatype\": \"BYTES\", \"data\": [ \"" + modPep + "\" ] }, { \"name\": \"precursor_charges\", " +
// "\"shape\": [ 1, 1 ], \"datatype\": \"INT32\", \"data\": [ "+ precursorCharge + " ] }, { \"name\": " +
// "\"collision_energies\", \"shape\": [ 1, 1 ], \"datatype\": \"FP32\", \"data\": [ "+ collisionEnergy +
// " ] }] }";
// }
else if (model.equals("Prosit_2020_intensity_TMT")){
modPep = "[UNIMOD:737]-" + modPep;
inputString = "{ \"id\": \"0\", \"inputs\": [ { \"name\": \"peptide_sequences\", \"shape\": [ 1, 1 ], " +
"\"datatype\": \"BYTES\", \"data\": [ \"" + modPep + "\" ] }, { \"name\": \"precursor_charges\", " +
"\"shape\": [ 1, 1 ], \"datatype\": \"INT32\", \"data\": [ "+ precursorCharge + " ] }, { \"name\": " +
"\"collision_energies\", \"shape\": [ 1, 1 ], \"datatype\": \"FP32\", \"data\": [ "+ collisionEnergy +
" ] }] }";
" ] }, { \"name\": \"fragmentation_types\", \"shape\": [ 1, 1 ], \"datatype\": \"BYTES\", \"data\": [ \"" +
fragmentMethod + "\" ] } ] }";
}

}
Expand Down Expand Up @@ -177,10 +186,20 @@ public MSnSpectrum getSpectra() throws IOException {
while ((responseLine = br.readLine()) != null) {
response.append(responseLine.trim());
}
String responseString = response.toString();
String collapsed = responseString;
if (responseString.contains("parameters")){
collapsed = responseString.substring(0, responseString.indexOf("\"parameters\":")) + responseString.substring(responseString.indexOf("},") + 2);
}

JSONObject jsonObject = new JSONObject(response.toString());
JSONObject jsonObject = new JSONObject(collapsed);
JSONArray output = jsonObject.getJSONArray("outputs");
JSONObject intObject = (JSONObject) output.get(0);
JSONObject intObject;
if (model.equals("AlphaPept_ms2_generic")){
intObject = (JSONObject) output.get(0);
} else {
intObject = (JSONObject) output.get(2);
}
JSONObject mzObject = (JSONObject) output.get(1);
List<Object> intensity = intObject.getJSONArray("data").toList();
List<Object> mzs = mzObject.getJSONArray("data").toList();
Expand All @@ -207,101 +226,109 @@ public MSnSpectrum getSpectra() throws IOException {
return spectrum;
}

// private void getSpectra() throws IOException {
// String url = "https://koina.proteomicsdb.org/v2/models/AlphaPept_ms2_generic/infer";
// usedURL = new URL(url);
//
// HttpURLConnection conn = (HttpURLConnection) usedURL.openConnection();
// conn.setRequestMethod("POST");
// conn.setRequestProperty("Content-Type", "application/json; utf-8");
// conn.setRequestProperty("Accept", "application/json");
// conn.setDoOutput(true);
//
// String jsonInputString = "{\n" +
// " \"id\": \"0\",\n" +
// " \"inputs\": [\n" +
// " {\n" +
// " \"name\": \"peptide_sequences\",\n" +
// " \"shape\": [\n" +
// " 1,\n" +
// " 1\n" +
// " ],\n" +
// " \"datatype\": \"BYTES\",\n" +
// " \"data\": [\n" +
// " \"AAAAAKAKM[UNIMOD:35]\"\n" +
// " ]\n" +
// " },\n" +
// " {\n" +
// " \"name\": \"precursor_charges\",\n" +
// " \"shape\": [\n" +
// " 1,\n" +
// " 1\n" +
// " ],\n" +
// " \"datatype\": \"INT32\",\n" +
// " \"data\": [\n" +
// " 2\n" +
// " ]\n" +
// " },\n" +
// " {\n" +
// " \"name\": \"collision_energies\",\n" +
// " \"shape\": [\n" +
// " 1,\n" +
// " 1\n" +
// " ],\n" +
// " \"datatype\": \"FP32\",\n" +
// " \"data\": [\n" +
// " 25\n" +
// " ]\n" +
// " },\n" +
// " {\n" +
// " \"name\": \"instrument_types\",\n" +
// " \"shape\": [\n" +
// " 1,\n" +
// " 1\n" +
// " ],\n" +
// " \"datatype\": \"BYTES\",\n" +
// " \"data\": [\n" +
// " \"QE\"\n" +
// " ]\n" +
// " }\n" +
// " ]\n" +
// "}";
//
// try(OutputStream os = conn.getOutputStream()) {
// byte[] input = jsonInputString.getBytes(StandardCharsets.UTF_8);
// os.write(input, 0, input.length);
// } catch (IOException e) {
// throw new RuntimeException(e);
// }
//
// int responseCode = conn.getResponseCode();
// System.out.println("Response Code : " + responseCode);
//
// try(BufferedReader br = new BufferedReader(
// new InputStreamReader(conn.getInputStream(), StandardCharsets.UTF_8))) {
//
// StringBuilder response = new StringBuilder();
// String responseLine = null;
// while ((responseLine = br.readLine()) != null) {
// response.append(responseLine.trim());
// }
//
// JSONObject jsonObject = new JSONObject(response.toString());
// JSONArray output = jsonObject.getJSONArray("outputs");
// JSONObject intObject = (JSONObject) output.get(0);
// JSONObject mzObject = (JSONObject) output.get(1);
// List<Object> intensity = intObject.getJSONArray("data").toList();
// List<Object> mzs = mzObject.getJSONArray("data").toList();
//
// for (int i = 0; i < intensity.size(); i++) {
// if ((double) intensity.get(i) > 0) {
// System.out.println(mzs.get(i) + " " + intensity.get(i));
// }
// }
//
// }
//
//
// }
private void getSpectra(String test) throws IOException {
String url = "https://koina.proteomicsdb.org/v2/models/AlphaPept_ms2_generic/infer";
usedURL = new URL(url);

HttpURLConnection conn = (HttpURLConnection) usedURL.openConnection();
conn.setRequestMethod("POST");
conn.setRequestProperty("Content-Type", "application/json; utf-8");
conn.setRequestProperty("Accept", "application/json");
conn.setDoOutput(true);

String jsonInputString = "{\n" +
" \"id\": \"0\",\n" +
" \"inputs\": [\n" +
" {\n" +
" \"name\": \"peptide_sequences\",\n" +
" \"shape\": [\n" +
" 1,\n" +
" 1\n" +
" ],\n" +
" \"datatype\": \"BYTES\",\n" +
" \"data\": [\n" +
" \"SKSEEAHAEDSVM[UNIMOD:35]DHHFR\"\n" +
" ]\n" +
" },\n" +
" {\n" +
" \"name\": \"precursor_charges\",\n" +
" \"shape\": [\n" +
" 1,\n" +
" 1\n" +
" ],\n" +
" \"datatype\": \"INT32\",\n" +
" \"data\": [\n" +
" 2\n" +
" ]\n" +
" },\n" +
" {\n" +
" \"name\": \"collision_energies\",\n" +
" \"shape\": [\n" +
" 1,\n" +
" 1\n" +
" ],\n" +
" \"datatype\": \"FP32\",\n" +
" \"data\": [\n" +
" 27\n" +
" ]\n" +
" },\n" +
" {\n" +
" \"name\": \"instrument_types\",\n" +
" \"shape\": [\n" +
" 1,\n" +
" 1\n" +
" ],\n" +
" \"datatype\": \"BYTES\",\n" +
" \"data\": [\n" +
" \"QE\"\n" +
" ]\n" +
" }\n" +
" ]\n" +
"}";

try(OutputStream os = conn.getOutputStream()) {
byte[] input = jsonInputString.getBytes(StandardCharsets.UTF_8);
os.write(input, 0, input.length);
} catch (IOException e) {
throw new RuntimeException(e);
}

int responseCode = conn.getResponseCode();
System.out.println("Response Code : " + responseCode);

try(BufferedReader br = new BufferedReader(
new InputStreamReader(conn.getInputStream(), StandardCharsets.UTF_8))) {

StringBuilder response = new StringBuilder();
String responseLine = null;
while ((responseLine = br.readLine()) != null) {
response.append(responseLine.trim());
}
String responseString = response.toString();
String collapsed = responseString;
if (responseString.contains("parameters")){
collapsed = responseString.substring(0, responseString.indexOf("\"parameters\":")) + responseString.substring(responseString.indexOf("},") + 2);
}
// System.out.println(response.toString());

JSONObject jsonObject = new JSONObject(collapsed);
JSONArray output = jsonObject.getJSONArray("outputs");
JSONObject intObject = (JSONObject) output.get(0);
JSONObject mzObject = (JSONObject) output.get(1);
JSONObject annoObject = (JSONObject) output.get(2);
List<Object> intensity = intObject.getJSONArray("data").toList();
List<Object> mzs = mzObject.getJSONArray("data").toList();
List<Object> anno = annoObject.getJSONArray("data").toList();

for (int i = 0; i < intensity.size(); i++) {
if ((double) intensity.get(i) > 0) {
System.out.println(mzs.get(i) + " " + intensity.get(i) + " " + anno.get(i));
}
}

}


}

}
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