Example usage for org.apache.commons.net.ftp FTPClient sendCommand

List of usage examples for org.apache.commons.net.ftp FTPClient sendCommand

Introduction

In this page you can find the example usage for org.apache.commons.net.ftp FTPClient sendCommand.

Prototype

public int sendCommand(String command, String args) throws IOException 

Source Link

Document

Sends an FTP command to the server, waits for a reply and returns the numerical response code.

Usage

From source file:base.BasePlayer.AddGenome.java

static void updateEnsemblList() {
    try {/*w  w w  .java  2s  .c o  m*/

        menu = new JPopupMenu();
        area = new JTextArea();
        menuscroll = new JScrollPane();

        area.setFont(Main.menuFont);

        menu.add(menuscroll);
        //menu.setPreferredSize(new Dimension(menu.getFontMetrics(Main.menuFont).stringWidth("0000000000000000000000000000000000000000000000000")+Main.defaultFontSize*10, (int)menu.getFontMetrics(Main.menuFont).getHeight()*4));
        menu.setPreferredSize(new Dimension(300, 200));

        //area.setMaximumSize(new Dimension(300, 600));
        //area.setLineWrap(true);
        //area.setWrapStyleWord(true);
        //area.setPreferredSize(new Dimension(300,200));

        area.revalidate();
        menuscroll.getViewport().add(area);
        menu.pack();
        menu.show(AddGenome.treescroll, 0, 0);
        /*   area.addMouseListener(new MouseListener() {
                
              @Override
              public void mouseClicked(MouseEvent arg0) {
                 // TODO Auto-generated method stub
                         
              }
                
              @Override
              public void mouseEntered(MouseEvent arg0) {
                 // TODO Auto-generated method stub
                         
              }
                
              @Override
              public void mouseExited(MouseEvent arg0) {
                 // TODO Auto-generated method stub
                         
              }
                
              @Override
              public void mousePressed(MouseEvent arg0) {
                 StringBuffer buf = new StringBuffer("");
                 for(int i= 0; i<(int)(Math.random()*100); i++) {
                    buf.append("O");
                 }
                 AddGenome.area.append(buf.toString() +"\n");
                 AddGenome.area.setCaretPosition(AddGenome.area.getText().length());
                 AddGenome.area.revalidate();
                         
              }
                
              @Override
              public void mouseReleased(MouseEvent arg0) {
                 // TODO Auto-generated method stub
                         
              }
                      
           });*/

        FTPClient f = new FTPClient();
        news = new ArrayList<String[]>();
        area.append("Connecting to Ensembl...\n");
        //System.out.println("Connecting to Ensembl...");
        f.connect("ftp.ensembl.org");
        f.enterLocalPassiveMode();
        f.login("anonymous", "");
        //System.out.println("Connected.");
        area.append("Connected.\n");

        FTPFile[] files = f.listFiles("pub");
        String releasedir = "";
        String releasenro;
        for (int i = 0; i < files.length; i++) {

            if (files[i].isDirectory() && files[i].getName().contains("release")) {
                releasedir = files[i].getName();
            }
        }

        files = f.listFiles("pub/" + releasedir + "/fasta/");
        releasenro = releasedir.substring(releasedir.indexOf("-") + 1);
        area.append("Searching for new genomes");
        for (int i = 0; i < files.length; i++) {
            if (files[i].isDirectory()) {
                FTPFile[] fastafiles = f
                        .listFiles("pub/" + releasedir + "/fasta/" + files[i].getName() + "/dna/");
                String[] urls = new String[5];
                for (int j = 0; j < fastafiles.length; j++) {
                    if (fastafiles[j].getName().contains(".dna.toplevel.")) {
                        urls[0] = "ftp://ftp.ensembl.org/pub/" + releasedir + "/fasta/" + files[i].getName()
                                + "/dna/" + fastafiles[j].getName();

                        String filePath = "/pub/" + releasedir + "/fasta/" + files[i].getName() + "/dna/"
                                + fastafiles[j].getName();
                        f.sendCommand("SIZE", filePath);
                        String reply = f.getReplyString().split("\\s+")[1];
                        urls[1] = reply;
                        break;
                    }
                }
                if (urls[0] == null) {
                    continue;
                }
                FTPFile[] annofiles = f.listFiles("pub/" + releasedir + "/gff3/" + files[i].getName());
                for (int j = 0; j < annofiles.length; j++) {
                    if (annofiles[j].getName().contains("." + releasenro + ".gff3.gz")) {
                        urls[2] = "ftp://ftp.ensembl.org/pub/" + releasedir + "/gff3/" + files[i].getName()
                                + "/" + annofiles[j].getName();
                        String filePath = "/pub/" + releasedir + "/gff3/" + files[i].getName() + "/"
                                + annofiles[j].getName();
                        f.sendCommand("SIZE", filePath);
                        String reply = f.getReplyString().split("\\s+")[1];
                        urls[3] = reply;
                        break;
                    }
                }
                if (urls[2] == null) {
                    continue;
                }
                if (files[i].getName().contains("homo_sapiens")) {
                    urls[4] = "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz";
                } else if (files[i].getName().contains("mus_musculus")) {
                    urls[4] = "http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/cytoBand.txt.gz";
                }
                String name = urls[0].substring(urls[0].lastIndexOf("/") + 1, urls[0].indexOf(".dna."));
                //System.out.print(urls[0]+"\t" +urls[1] +"\t" +urls[2] +"\t" +urls[3]);
                if (genomeHash.containsKey(name) || AddGenome.removables.contains(name)) {
                    //System.out.println(name +" already in the list.");
                    area.append(".");
                } else {
                    area.append("\nNew genome " + name + " added.\n");
                    AddGenome.area.setCaretPosition(AddGenome.area.getText().length());
                    AddGenome.area.revalidate();
                    //System.out.println("New reference " +name +" found.");
                    organisms.add(name);
                    news.add(urls);

                    if (urls[4] != null) {
                        //System.out.println(urls[0] +" " + urls[2] +" " +urls[4]);
                        URL[] newurls = { new URL(urls[0]), new URL(urls[2]), new URL(urls[4]) };
                        genomeHash.put(name, newurls);
                    } else {
                        URL[] newurls = { new URL(urls[0]), new URL(urls[2]) };
                        genomeHash.put(name, newurls);
                    }
                    Integer[] sizes = { Integer.parseInt(urls[1]), Integer.parseInt(urls[3]) };
                    sizeHash.put(name, sizes);

                }
                /*if(urls[4] != null) {
                   System.out.print("\t" +urls[4]);
                }
                System.out.println();
                */
            }

        }

        checkGenomes();
        if (news.size() > 0) {

            try {
                //File file = new File();
                FileWriter fw = new FileWriter(Main.genomeDir.getCanonicalPath() + "/ensembl_fetched.txt");
                BufferedWriter bw = new BufferedWriter(fw);

                for (int i = 0; i < news.size(); i++) {
                    for (int j = 0; j < news.get(i).length; j++) {
                        if (news.get(i)[j] == null) {
                            break;
                        }
                        if (j > 0) {
                            bw.write("\t");
                        }
                        bw.write(news.get(i)[j]);
                    }
                    bw.write("\n");
                }
                bw.close();
                fw.close();

            } catch (IOException e) {

                e.printStackTrace();
            }

        }
    } catch (Exception e) {
        Main.showError(e.getMessage(), "Error");
        e.printStackTrace();
    }

}