From 49228c2c4e16489dad8308eb990ea0461207f0b2 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 11 Feb 2019 09:11:22 +0100
Subject: [PATCH] old unused code removed
---
.../services/annotators/TairAnnotator.java | 37 -------------------
1 file changed, 37 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index 3f72c60466..60391fcae0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -5,8 +5,6 @@ import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.springframework.stereotype.Service;
@@ -39,11 +37,6 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
*/
private static Logger logger = Logger.getLogger(TairAnnotator.class);
- /**
- * Pattern used for finding UniProt symbol from TAIR info page .
- */
- private Pattern tairToUniprot = Pattern.compile("UniProtKB=([^-\"]*)");
-
/**
* Default constructor.
*/
@@ -92,17 +85,6 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
}
}
- /**
- * Returns URL to TAIR page about TAIR entry.
- *
- * @param tairId
- * TAIR identifier
- * @return URL to TAIR page about the TAIR entry
- */
- private String getTairUrl(String tairId) {
- return "https://arabidopsis.org/servlets/TairObject?type=locus&name=" + tairId;
- }
-
/**
* Returns URL to UniProt result containing mapped UniProtIds for submitted TAIR
* entry.
@@ -116,23 +98,6 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
+ "%29&format=list&columns=id";
}
- /**
- * Parse TAIR webpage to find information about {@link MiriamType#UNIPROT} and
- * returns them.
- *
- * @param pageContent
- * tair info page
- * @return uniprot identifier found on the page
- */
- private Collection<MiriamData> parseUniprot(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = tairToUniprot.matcher(pageContent);
- if (m.find()) {
- result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));
- }
- return result;
- }
-
/**
* Parse UniProt result page which contains list of Uniprot ids mapped to
* submitted TAIR id. The procedure obtains first {@link MiriamType#UNIPROT} and
@@ -174,10 +139,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
}
try {
- // String accessUrl = getTairUrl(tair.getResource());
String accessUrl = getUniProtUrl(tair.getResource());
String pageContent = getWebPageContent(accessUrl);
- // Collection<MiriamData> collection = parseUniprot(pageContent);
return parseUniprotUniprot(pageContent);
} catch (WrongResponseCodeIOException exception) {
logger.warn("Wrong reponse code when accessing tair data with id: " + tair.getResource());
--
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