[med-svn] [tn-seqexplorer] 01/01: Add diff against http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/Tn-seqExplorer1.5a-source_codes_and_libraries.zip.zip as patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository tn-seqexplorer.

commit 90627f72159bb4acdeeb38a4b745fa7c52e9b659
Author: Andreas Tille <tille at debian.org>
Date:   Mon May 8 12:51:42 2017 +0200

    Add diff against http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/Tn-seqExplorer1.5a-source_codes_and_libraries.zip.zip as patch
---
 debian/patches/active_genbank.patch | 88 +++++++++++++++++++++++++++++++++++++
 debian/patches/series               |  1 +
 2 files changed, 89 insertions(+)

diff --git a/debian/patches/active_genbank.patch b/debian/patches/active_genbank.patch
new file mode 100644
index 0000000..6c394b5
--- /dev/null
+++ b/debian/patches/active_genbank.patch
@@ -0,0 +1,88 @@
+Description: Diff against
+   http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/Tn-seqExplorer1.5a-source_codes_and_libraries.zip.zip
+
+--- a/src/GUI/SelectFNA.java
++++ b/src/GUI/SelectFNA.java
+@@ -152,7 +152,7 @@ public class SelectFNA extends JFrame {
+ 								ftp.connect("ftp.ncbi.nih.gov");
+ 								ftp.enterLocalPassiveMode();
+ 								ftp.login("anonymous", "");
+-								FTPFile[] files = ftp.listFiles("/genomes/archive/old_genbank/Bacteria/");
++								FTPFile[] files = ftp.listFiles("/genomes/Bacteria/");
+ 
+ 								firstLevelCombo.removeAllItems();
+ 								for (FTPFile t : files) {
+@@ -208,7 +208,7 @@ public class SelectFNA extends JFrame {
+ 								ftp.connect("ftp.ncbi.nih.gov");
+ 								ftp.enterLocalPassiveMode();
+ 								ftp.login("anonymous", "");
+-								String ftpDir = "/genomes/archive/old_genbank/Bacteria/" + firstLevelCombo.getSelectedItem() + "/";
++								String ftpDir = "/genomes/Bacteria/" + firstLevelCombo.getSelectedItem() + "/";
+ 								FTPFile[] files = ftp.listFiles(ftpDir);
+ 								ftp.disconnect();
+ 
+@@ -301,7 +301,7 @@ public class SelectFNA extends JFrame {
+ 							ftp.connect("ftp.ncbi.nih.gov");
+ 							ftp.enterLocalPassiveMode();
+ 							ftp.login("anonymous", "");
+-							String ftpDir = "/genomes/archive/old_genbank/Bacteria/" + firstLevelCombo.getSelectedItem() + "/";
++							String ftpDir = "/genomes/Bacteria/" + firstLevelCombo.getSelectedItem() + "/";
+ 							FTPFile[] files = ftp.listFiles(ftpDir);
+ 
+ 							File gbkTemp = null;
+--- a/src/GUI/MainFrame.java
++++ b/src/GUI/MainFrame.java
+@@ -328,7 +328,7 @@ public class MainFrame extends JFrame {
+ 							ftp.connect("ftp.ncbi.nih.gov");
+ 							ftp.enterLocalPassiveMode();
+ 							ftp.login("anonymous", "");
+-							String ftpDir = "/genomes/archive/old_genbank/Bacteria/" + ftpFirstLevelCombo.getSelectedItem() + "/";
++							String ftpDir = "/genomes/Bacteria/" + ftpFirstLevelCombo.getSelectedItem() + "/";
+ 							FTPFile[] files = ftp.listFiles(ftpDir);
+ 
+ 							for (FTPFile t : files){
+@@ -382,7 +382,7 @@ public class MainFrame extends JFrame {
+ 								ftp.connect("ftp.ncbi.nih.gov");
+ 								ftp.enterLocalPassiveMode();
+ 								ftp.login("anonymous", "");
+-								String ftpDir = "/genomes/archive/old_genbank/Bacteria/" + ftpFirstLevelCombo.getSelectedItem() + "/";
++								String ftpDir = "/genomes/Bacteria/" + ftpFirstLevelCombo.getSelectedItem() + "/";
+ 								FTPFile[] files = ftp.listFiles(ftpDir);
+ 
+ 								for (FTPFile t : files){
+@@ -537,7 +537,7 @@ public class MainFrame extends JFrame {
+ 							ftp.connect("ftp.ncbi.nih.gov");
+ 							ftp.enterLocalPassiveMode();
+ 							ftp.login("anonymous", "");
+-							FTPFile[] files = ftp.listFiles("/genomes/archive/old_genbank/Bacteria/");
++							FTPFile[] files = ftp.listFiles("/genomes/Bacteria/");
+ 
+ 							ftpFirstLevelCombo.removeAllItems();
+ 							for(FTPFile t : files){
+@@ -591,7 +591,7 @@ public class MainFrame extends JFrame {
+ 								ftp.connect("ftp.ncbi.nih.gov");
+ 								ftp.enterLocalPassiveMode();
+ 								ftp.login("anonymous", "");
+-								String ftpDir = "/genomes/archive/old_genbank/Bacteria/" + ftpFirstLevelCombo.getSelectedItem() + "/";
++								String ftpDir = "/genomes/Bacteria/" + ftpFirstLevelCombo.getSelectedItem() + "/";
+ 								FTPFile[] files = ftp.listFiles(ftpDir);
+ 								ftp.disconnect();
+ 
+@@ -798,7 +798,7 @@ public class MainFrame extends JFrame {
+ 			public void mouseClicked(MouseEvent arg0) {
+ 				JOptionPane.showMessageDialog(MainFrame.this, "This will guide you to finding the protein-coding (.ptt file) and RNA (.rnt file) gene\n"
+ 						+ "annotation at the FTP server of the National Center for Biotechnology Information\n"
+-						+ "(ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/)");
++						+ "(ftp://ftp.ncbi.nih.gov/genomes/)");
+ 			}
+ 		});
+ 		lblNeedHelp.setToolTipText("Click me!");
+@@ -1858,7 +1858,7 @@ public class MainFrame extends JFrame {
+ 			public void mouseClicked(MouseEvent arg0) {
+ 				JOptionPane.showMessageDialog(MainFrame.this, "The FASTQ file contains your sequence reads and you should have received it from Illumina or the sequencing facility\n"
+ 						+ "you used. The FNA file contains the genomic DNA sequence in fastA format and you can download it for complete\n"
+-						+ "prokaryotic genomes from the NCBI ftp server at ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/");
++						+ "prokaryotic genomes from the NCBI ftp server at ftp://ftp.ncbi.nih.gov/genomes/Bacteria/");
+ 			}
+ 		});
+ 		label_4.setToolTipText("Click me!");
diff --git a/debian/patches/series b/debian/patches/series
index 545c2cd..e2b1efa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 libjgoodies-from-java.patch
+active_genbank.patch

-- 
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